From a performance standpoint, I would take the time to cut out (or make!) your resources in manageable objects that you could use to assemble your levels in C2's editor. You would drastically improve memory load and file sizes. That, and it'll be easier to make changes later. The temptation to fully make your levels in Photoshop is there, but I would suggest avoiding that route. I don't necessarily mean tiles, though that is a wonderful option for many, but making smaller and more flexible objects is something you would thank yourself for later.
Also, I feel it increases the likelihood of completing the game--a very real concern for indie developers.