I do this all the time, I put them on one at a time if they are layered or are very near each other and have never had a problem with it. I have used many different brands and have never had a problem with any of them. Just be sure not to overheat it when in layers (bubbling can occur if it overheats, I have seen and even redone LOTS of sports uniforms out there with this problem.) Of course, always be sure to use a teflon sheet to protect any areas on the first layer(s) that are not protected by your next layer. If you are printing onto nylon, let the item completely cool before adding the next layer.
To do multi color overlay...cut the colors to overlap slightly-unless you can be dead on perfect to align them. Usually just pulling off the backing on the first color tweaks the shirt out of 'square' and you can't align perfect pieces. So cut oversize. Reset your press time to half, practice a little. All you want is enough time to tack down the colors, one at a time. Heat, peel quick, then lay down the next color. When you have all colors tacked down, the 'last' color done gets full press time. Occasionally if you figure the design right, you can cut excess backing out of the way and stick multi colors all together...I've done it. But printing and diecutting full color on the versacamm saves a lot of time. You can diecut each individual piece-don't need to do it as a 'patch' if you have time to do the weeding.