You can create a stereo track (interleaved) and you will be able to select the input sources that feed that track say Inputs 1&2. That will give you one track to deal with from then on and in that sense it is easier.
But you can create two mono tracks instead and select Input 1 to feed one mono track and Input 2 to feed the other mono track. The main reason for doing this though is the ability to pan around the left and right channels anywhere into your stereo field. But Cakewalk make a great plugin called Channel Tools and it can do all of those things on one stereo track only.
If you do use two mono tracks it is a bit of a pain because if you insert a plugin on them you will have to insert two plugins. One for each track. Then you will have to copy the setting from one plug to the adjacent one too. Same goes for dynamics processing or anything really.
Whereas a stereo track only needs one plug in on it and it is using the stereo version of the plug automatically but you only have to think one thing though.
Channel Tools lets you pan the left and right channels anywhere which is very handy. Normally they hard left and hard right but sometimes it is nice to narrow and move the stereo image around a bit to suit your mix.