How to rig a ship model is, of course, entirely up to the individual modeler. I would point out, though, that rigging line is one of the cheapest components of the model. Three or four sizes of each color (black and natural) won't cost significantly more than two sizes - and, obviously, the number of sizes won't have any effect whatever on the amount of time it takes.
Regarding ratlines, I have three alternatives to suggest. (I'm not a fan of the Heller/Airfix "loom," but if that's the route you want to go - for heaven's sake don't let me talk you out of it.)
First let's get some basic vocabulary out of the way. We're actually talking about two pieces of rigging. The shrouds are the near vertical lines that support the masts (and play a key role in transferring the energy of the wind in the sails to the hull, thereby pulling the ship through the water). The ratlines are much thinner pieces of rope that run horizontally across the shrouds; the sole purpose of the ratlines is to provide a "ladder" for the men climbing aloft. In reality, each ratline has an eyesplice worked into each end of it; the eyesplices are lashed to the foremost and aftermost shroud. The ratline itself is tied to each intervening shroud with a very simple knot called the clove hitch.
Aesthetically, it's important that the ratlines be a lot smaller in diameter than the shrouds. (That's one of several reasons why the plastic, or plastic-coated-thread, shroud/ratline assemblies in kits invariably look so hokey.)
There are two traditional ways to rig ratlines on a model. The first is the one Jake suggested: tie the ratlines by hand to the shrouds. (I don't think anybody would seriously suggest actually working eyesplices into the ends, but a good compromise is to use a reef knot - aka square knot - on each end and clove hitches on the others.
The last model on which I rigged ratlines by hand was my little model of the frigate Hancock , on 3/32"=1' scale. (That's 1/128 - slightly larger than the Academy Cutty Sark.) I made the shrouds of silk thread, spun up on a primitive "rope-making machine," and the ratlines of nickel-chromium wire. I'm pretty satisfied with the results ( http://www.hmsvictoryscalemodels.be/JohnTilleyHancock/index.html ). In all honesty, though, built that model almost thirty years ago and I'm not at all sure my current set of 59-year-old fingers and eyeballs would be up to the task now. (Admittedly the Hancock had a lot more shrouds and ratlines than the Cutty Sark, but when I look at that old model now I have to admit I have trouble focusing on those clove hitches.) If you want to try it by all means do so - but if you find it's a bit much, for heaven's sake don't feel bad about it.
Method #2 is the old "needle-through-the-shroud" system. It's been described several times here in the Forum, and can produce a good, neat-looking result. (And only those observers with excellent short-range eyesight will be able to tell the difference.)
The third method I want to recommend for consideration is one that a lot of modelers reject out of hand - and I don't think they should. That method is to rig the shrouds to scale (or nearly so) and leave the ratlines off. One of the golden rules is to omit stuff that's too small to be replicated to scale. Many excellent, knowledgeable modelers working on small scales have taken that approach, and the truth is that a model without ratlines is capable of being made to look really good. To my eye, a model with no ratlines that's otherwise built carefully to scale looks far better than one with overly-heavy ratlines spaced too far apart.
But it's all up to the individual modeler.
Hope that helps a little. Good luck.