One obvious point needs to be born in mind in any such discussion: it's your model and you don't "have" to do anything to it. There are, fortunately, no rules in the hobby of ship model building.
There are several ways to approach the matter of rigging. "Standing rigging" is usually defined as the rigging that holds up the masts. (Without it they'll fall over.) "Running rigging" is the gear that's used to move the yards, gaffs, booms, etc. and the sails in order to maneuver the ship. Running rigging can be further divided into three sub-categories. Some lines are used to raise and lower the yards and swing them around to receive the wind. These lines are virtually essential just to keep all the spars in position. They include halyards, lifts, braces, and the gear associated with the gaff and boom on the mizzenmast. It would be extremely unusual to see a ship without them.
The second category of running rigging is attached to the sails, and is used to set and furl them and change their orientation in various ways. The lines in that category include sheets, clewlines, buntlines, bowlines, jib and staysail halyards and downhaulers, slablines, reef tackles, and quite a few others. If a ship was to be at anchor or tied up to a pier for a long time, the sails might well be removed from the yards and stowed - and that sort of rigging might well be removed with them.
The third group of running rigging lines has miscellaneous purposes not directly related to the movement of the ship - gear for cargo handling, flag halyards, anchor gear, etc.
Lots of modelers, taking into consideration such matters as scale, time, and personal taste, adopt a compromise approach to running rigging. Many perfectly respectable models have been built with just the running rigging in what I've just dubbed Category #1. Those lines, in lots of people's eyes, make the model look reasonably believable and complete. To do the ones in Category #2 it's desireable - indeed almost necessary - to fit the model with sails. (Some modelers, including me, like the look of furled sails.) In the absence of the sails, you have to do some odd things with the lines that normally would be attached to them - bowlines, reef tackles, clewlines, leechlines, etc. It's possible to tie those lines off at points other than the sails, but a model rigged that way can look pretty bewildering.
Category #3 is pretty simple. You'll almost certainly want to rig the flag halyards, and the yard and stay tackles, which are used for handling the ship's boats and other objects, are fairly straightforward. You can show the anchors stowed at the bow, or include some or all of the gear that's used for handling them.
If you don't have a lot of experience with this sort of thing, a workable approach might be to start by setting up the standing rigging and the running gear in Category #1. Then sit back, imbibe some liquid refreshment, and ask yourself two questions: how does the model look to me, and how much more time do I really want to spend on it? If you're satisfied with it, that's what matters most. If you want to add more rigging to it, you certainly have the option of doing so.
But it's all up to you. Go to a good maritime museum and you'll see all sorts of variations on the theme of rigging in ship models - including some beautiful examples that don't have masts or rigging at all.
I agree with Scottrc about the Heller rigging instructions. In fact I'll go a step further: they're garbage. They have three basic problems. First, the English translation is a scandal. (It apparently was written by somebody who neither understood French nor had attempted to build the model.) Second, the designers adopted a system of cryptic diagrams and numbers that makes the job at least twice as confusing as it needs to be. Third, the people responsible didn't understand how rigging works. In one of the great howlers in the history of ship model kits, they made no provision for securing the yards to the masts. That's downright laughable.
Rigging this model will be a lot easier if you get hold of at least one good book. The Victory has been the subject of quite a mass of literature over the years. Three books include good, comprehensive rigging diagrams for her: John McKay's Anatomy of the Ship: The 100-Gun Ship Victory; Alan McGowen's H.M.S. Victory: Construction, Career and Restoration (with drawings by the same Mr. McKay); and C. Nepean Longridge's classic The Anatomy of Nelson's Ships. All three are excellent works. I think, though, that my first recommendation would be the Longridge book. Despite the title, it's a detailed account of how the author built his 1/48-scale model of the Victory (which is regarded as a classic - and doesn't by any means include all the prototype's running rigging). The drawings in it are beautiful and easy to understand. Best of all, Longridge provides a verbal explanation of how each line leads. To me, at least, that's preferable to a diagram that makes me sort out a bunch of numbers. (Mr. McKay's drawings are masterpieces of the drafting art, but the rigging diagrams have little accompanying text - and only in rare cases to both ends of a line appear in the same drawing.)
One other thing you may want to bear in mind when you get to the rigging stage. The blocks and deadeyes in the kit are just about worthless. In a sense that isn't really Heller's fault. A scale block or deadeye has to have a groove around it and at least one hole through it. Styrene parts have to be made in rigid molds, and a rigid two-piece mold can't produce an object with a groove around it and a hole through it. Most serious modelers who tackle this kit junk the blocks and deadeyes and replace them with either wood or metal aftermarket parts. (My personal favorites are the ones made by Bluejacket - www.bluejacketinc.com .) Other candidates for aftermarket part replacement are the belaying pins, hammock netting stanchions, and eyebolts. Some (not all) of the belaying pins in the kit have sharp points (pure silliness), and eyebolts and hammock netting stanchions snap pretty easily when put under a strain. Bluejacket sells nice brass belaying pins, and perfectly acceptable stanchions and eyebolts can be made from brass wire in a few minutes.
None of the foregoing is intended to detract from the fact that the Heller Victory is an excellent kit - one of the best products of the hobby industry. Most of its problems are due to the inherent weaknesses of styrene as a material and to the limitations of the injection-molding process. With the help of some aftermarket parts, a little basic scratchbuilding, and some good reference material to replace those wretched instructions, it can be turned into a masterpiece.
Good luck.