Basically one just comes with more power stock than the other. The 4bta has an aftercooler and is rated at around 130 hp. The 4bt doesn't have an aftercooler and is usually rated at 105-110 hp. Mechanically the engines are identical (except for possibly compression ratio and the aftercooler of course). If the engine has a air/water aftercooler I think it is a little bit taller than the standard 4bt.
So it comes down to how much power you are looking for. You can always add an aftercooler to a 4bt. I see more 4bts for sale than 4bta.
Do some research on this site and you'll find alot of info about swapping this engine. There are several people who have done/are working on the same swap as you. Check the buildup threads I know there's at least 1 jeep in there.