Personally, I find the setting up of deadeyes just about the most challenging part of rigging a ship model. The job is made worse by the fact that it has to be done so early in the rigging process.
I don't know of a really good way to do it. People have come up with various jigs and fixtures that attempt to keep the deadeyes in straight rows while the lanyards are being rigged. Such things help. But if the tension on the lanyards isn't consistent from shroud to shroud, the deadeyes will get whopperjawed as soon as the jig is removed.
Some people try setting up the lanyards before the shrouds are secured at their upper ends. That method may be helpful for some, but I find that it makes it difficult to set up the shrouds with uniform tension.
The way I usually do it is as follows (and I don't claim this method is particularly good).
1. Cut a piece of the heavy line that's going to be the shroud to something more than its final length - including the parts that will be seized around the deadeyes. (I'm assuming we're dealing with a "normal" shroud that starts at a deadeye, goes around the masthead, and comes down to another deadeye on the same side of the ship.) Seize one end of it around a deadeye.
2. Rig the lanyard. Tie a big knot in the end of it. (The traditional full-size one is the Matthew Walker knot, but on a model several reef knots tied on top of each other will work better.) Start rigging the lanyard by passing the lanyard outward through the upper lefthand hole (as viewed from inboard) in the upper deadeye. (Caveat: if the shroud is cable-laid - i.e., lefthand twist - the lanyard starts through the upper righthand hole.) Then it goes inboard through the upper righthand hole (as viewed from outboard) of the first lower deadeye. Then to the center hole in the upper deadeye, and so on. By the time you get the lanyard through the last hole, you'll find that the whole spindly-looking arrangement is actually pretty sturdy. It will be surprisingly difficult to pull the end of the lanyard through the deadeyes. Those old riggers knew what they were doing.
On ships of most periods, the distance from the upper deadeye to the lower should be about three times the deadeye diameter. Good news for modelers of Columbus-period ships, though: I've seen quite a few contemporary pictures (and competent modern paintings) that show pretty sloppy-looking deadeyes, with some pairs quite a bit farther apart than others.
Secure the bitter end of the lanyard. There are various ways to do this. Some sources say the end of the lanyard should be seized back on itself. Others say the end should be "expended in half hitches" around the lower end of the shroud, just above the upper deadeye. On a model, this is unlikely to make much difference.
3. Pass the end of the shroud (or, more properly, shroud pair) up through the lubber's hole in the top (if any), around the masthead, down through the lubber's hole again, and down toward the second deadeye that's waiting in the channel. Here's where the job starts to get tricky. Try to judge where on the length of the second shroud the deadeye belongs, and seize it there. You want the upper deadeyes to be in line with each other, and the two shrouds to be reasonably taut. When you're satisfied that you have the deadeye in the right place on the shroud, seize it in place and find out whether it's in line with the adjacent deadeye.
4. Rig the second lanyard. If you've done everything right, the deadeyes will be in line and the two shrouds will be just about equal in tautness.
5. Seized the two shrouds together just below the masthead. (This is how I do it myself; I'm sure others will seize the shrouds earlier in the proceedings.) Now the shrouds should be quite taut. They may, in fact, make the mast lean over a little. That's ok; the shrouds and lanyards on the other side of the ship will pull it back. When you've set up all the shrouds, the mast may lean slightly backwards. That's ok too; you can pull it into line with the stay.
By the time all the lower standing rigging is in place, you should be rewarded by a neat, symmetrical set of deadeyes and shrouds that twang slightly when you tweak them.
Here, as elsewhere in the rigging process, there's just no substitute for practice. I find that, since I build slowly, and years often pass between rigging jobs, my fingers have to relearn the process every time I do it. (Yes, fingers learn - and forget. Believe me.) But nothing makes a model look better than a nice set of shrouds deadeyes, lanyards, and ratlines,
Hope all that helps a little. Good luck.