Yes it can split them as long as you have everything marked.  To split the return, highlight it on the homebase view and go to file, split MFJ return.  

ProSeries will not transfer the Driver license, Bank info and in the case of Ohio returns, the County lived in, when it splits the return.

In case you haven't used it, there is a MFJ vs MFS Estimated worksheet for Federal and State so you can check which way is better, before doing the actual "Split MFS Return" I use it to check on all my MFJ returns.