Maybe a little basic terminology would be helpful here.
Standing rigging stands. With a few exceptions (extremely few in a latter-day sailing ship like the Cutty Sark), it doesn't "run" through blocks or other gadgets; it only gets moved around when it's being set up or tightened. Its purpose is to keep the masts from falling down, and to transmit the forces exerted by the wind to the ship's hull. (The wind fills the sails; the sails exert force on the yards and masts; and the masts, by means of the standing rigging, pull the ship through the water.)
Running rigging runs. It's constantly being hauled around, by means of blocks, winches, and other gear, to make various parts of the ship move in response to the wind and the commands of the people operating the ship.
Running rigging can be divided, for purposes of discussion, into three sub-categories. One - lines that support and adjust movable spars (i.e., yards, gaffs, and booms). These include braces (which swing the yards in a horizontal plane), halyards (which haul the various spars up and down when the sails are set and furled), and lifts (which are secured to the ends of the spars, to maintain them at the desired angles relative to the masts). These lines are, generally speaking, permanent parts of the ship's rigging, and are rarely if ever removed.
Two - lines that control the sails. These include sheets, tacks, buntlines, clewlines, leechlines, bowlines, reef tackles, and a few others. These lines are directly associated with the sails. Some of them might well be removed when the sails were removed (i.e., when the ship was to be laid up for a prolongued period).
Three - lines used for various purposes not directly related to the spars and sails. These include boat davit falls, cargo handling gear, etc. The cargo handling gear normally was only set up when the ship was loading or unloading. (Those big black winches at the feet of the fore- and mainmasts were for handling cargo.)
The triangular sails between the masts are called staysails. The running rigging associated with them isn't really so complicated, but it may be a little confusing. Each staysail has a pair of sheets leading from its lower, after corner (one on each side, coming into play depending on the direction of the wind), a halyard running up from its upper corner (to haul the sail up the stay when it's being set), a downhauler running down from the upper corner (to haul the sail down when it's being furled), and a tack on the forward bottom corner (to secure that corner, so the halyard can stretch the sail taut).
How much rigging you put on your model is, of course, entirely up to you. One popular approach for models without sails is to include the standing rigging and the "category one" running rigging. That configuration secures a line to almost every conspicuous point, so the ship looks reasonably complete; the spars don't seem to stick out in space with nothing to support or control them. The real ship might look like this if she were laid up for a fairly long period. In real life it would be quite unusual for all the lines in "category two" to be removed, but lots of eminently respectable models are rigged this way. This is the approach I'd probably recommend to anybody who doesn't have a fair amount of practice with rigging.
There's one important point that lots of newcomers miss. The yards of a sailing ship don't just swing around horizontally; they slide up and down the masts. The exceptions (in this particular case) are the lower yards and the lower topsail yards, which are fixed permanently into their positions. The Cutty Sark has double topsails. The upper topsail yard on each mast slides up and down the topmast - up when the sail is set, down when it's furled. (Any photo of the ship with the sails either furled or removed should make this clear. The upper and lower topsail yards are only a few feet apart.) The topgallant, royal, and main skysail yards also slide up and down. If the sails aren't present, the yards should be in their lowered positions. (If I remember right, Revell molded some rings around the mast components to indicate both raised and lowered yard positions. I don't know whether the instructions in Repulse145's kit explain all this or not; those in early versions of the kit did.) Putting the yards in their raised positions with no sails set is a mark of a modeler who doesn't entirely understand how rigging works.
The Cutty Sark's yards have fixed lifts. (They're made out of wire. They could, in fact, almost be included in the standing rigging; they don't run through blocks.) The lifts of the lower and lower topsail yards are taut all the time. When the upper topsail, topgllant, royal, and skysail yards are raised to set the sails, the lifts go slack and droop down behind the sails. If you're omitting the sails and rigging the yards in their lowered positions, all the lifts should be taut.
If you're omitting the sails (which I personally think is a good idea; I've never been a fan of vac-formed plastic sails) you can forget about the staysail rigging - and, for that matter, the running rigging of the headsails, between the foremast and the bowsprit. But that's entirely up to you.
As for knots - don't lose any sleep over the subject. Knots are a fascinating, fun subject; people have invented hundreds (or maybe thousands) of them over the centuries. But for ship modeling you only need to learn two - or maybe only one.
The basic knot used to secure a line to a spar or other is the reef knot, known to landlubbers as the square knot. In order to rig a ship model you really need to know how to tie that one; it would be hard, if not impossible, to get along without it. You probably already know how to tie it.
If you're going to rig your own ratlines you need to learn the clove hitch. It's an extremely simple knot; you can learn it in a couple of minutes. (Knots are notoriously difficult to describe verbally, so I won't try, but a picture of a clove hitch will make it ludicrously obvious.)
If you discard the kit's plastic "deadeye and lanyard assemblies" and rig your own shroud lanyards, you'll need some sort of "stopper knot" to keep the end of the lanyard from slipping through the deadeye; on 1/96 scale a reef knot with two or three extra loops in it will do the job fine. Rigging individual deadeyes and lanyards is tricky; I don't recommend it for newcomers.
If you're interested in such things, a text like The Ashley Book of Knots will keep you busy for a long time, and learning additional knots can be lots of fun. But for ship modeling they aren't really necessary.
I've said it before and I'll say it again: the best possible way to find out about the Cutty Sark's rigging (and every other feature of her) is to get hold of a set of those plans by George Campbell. Two of the three sheets are devoted to the rigging and sails. There's no better bargain for ship modelers.
Hope that helps a little. Good luck.