Shock length can be made to be 50% up, 50% down or biased to one or the other. Personally, I like to keep it close to 50-50.
1) Make sure your bumpstops are adjusted properly so that nothing is hitting and you aren't binding up the coils. If you haven't done this, it is essential to having a properly functioning suspension and finding what your shock lengths need to be.
2) Put your axle to full bump and measure the distance between the upper and lower shock mounts. This is roughly the compressed length your shocks will need to be if you don't want to add anymore bumpstop to your rig. If the compressed length is longer than this, you will need to add bumpstop to avoid damaging your shocks.
3) Measure the unloaded length of your coils. You're shocks don't need to have an extended length any longer than this because it will just allow your coils to unseat which is useless.
4) Go shopping for some shocks that match you're compressed and extended length needs. Keep in mind they don't have to be dead nuts on the lengths you obtained from your measurements, but you should try to keep them as close as possible to those lengths.
Edit: This site seems to have a very good selection and gives you an idea of the different lengths that the Bilsteins offer http://www.shockwarehouse.com/site/bst_5100.cfm
4wheelparts.com also has a good selection of bilsteins that are valved for TJ's so there's no guess work for you to do