Javon,
As a wholesaler I'm guessing that you don't have to be on the money with your repair costs, you just need to be in the ballpark.
Square footage should work fine for a quick and dirty estimate but not on the total sf of the house. Like Mike G said you have to figure out exactly what needs to be fixed. Then you should be able to apply sf, linear ft, or unit costs to each of those items and add up a total. For example, 500sf wood floor @x/sf + 400sf carpet @y/sf, + (6) interior doors @ z/each, etc. = $XXXXX.00
The best way to find these prices is to ask local installers but if you don't want to do that you can use a construction cost provider like RSMeans. Check out their Residential Cost Data book. (no affiliation) Its like $90 on Amazon.
When using a construction cost data you have to realize that it is just a baseline, its not going to be right on. But if you're thorough on your takeoffs you should be close enough, its been my experience that most of these prices will be higher anyways.
The key to successful estimating is the same for any business, measure and adjust. If you do a deal, follow up with your buyer to see what the rehab ended up costing. How close was your estimate to his/her actual cost? Was it higher or lower? By what %?
Like Tim G said, you'll get the hang of it after a few.