It's a much better idea to keep them separated. Firstly, you definitely have to quarantine any new snake just in case they have anything like parasites or diseases that aren't initially apparant.

But even assuming that the second snake was 100% healthy, if you house two snakes together, you'll have a very difficult time figuring out which one pooped. Snakes can become stressed very easily, especially when housed together, and stress can cause all sorts of problems.

If one snake is on in the basking area and the other is on the cold side, is that because he just wanted to be a little cooler, or was he ousted by the more dominant snake in the basking area, or vice versa? Is one hiding and the other exploring because that's what they want to do, or are there unseen struggles for dominance?