First off, you do not HAVE to fill out every profile, or create ANY profiles. They are just aids to be used or not. They can save time so you don't have to fill in repetitive info on each and every listing. Which ones you use depends on the variablity and repetitiveness of your listings.
What I do on shipping is add a shipping profile to my master profile so that it loads along with my other profiles(I don't even use an "item" profile as I have no repetitive item information). I fill in a shipping cost in my shipping profile, but since my costs are different with each listing, I simply change that amount manually after it loads. The rest of the shipping info I leave alone(item location, country shipped to,insurance info, etc.)
So you could do the same - fill in a cost for each option in your shipping profile, then after you have loaded the profile into your listing, replace those costs with your actual costs as you work up your listing. Do that each time you do a listing.
Remember, any info loaded into your listing by your profiles can then be changed, just as if you had entered the info manually. Also if you discover a mistake after posting, you can always change it in your active listing, subject to ebay's rules on changes of course.