You need to prevent both devices from syncing automatically when you connect them to the PC.
Once you have that set, try this.
The above is not absolutely necessary but I prefer it that way.
I have one main computer (a pc) but i have two ios devices (an iphone and an ipad). I use the iphone and the ipad for different reasons so they have different apps, songs, vids, etc. Is there a way that i can keep all the apps, song, vids, etc. from the iphone separate from the ones in the ipad?