textures are located in seperate files (all the GCT does is read from them), so yes, you'll be able to keep your textures.
As for storing multiple GCTs, I suggest simply making some extra folders to store them in (since they all have the same name and thus cannot be stored in the SAME folder, unles you want to keep renaming them every time you switch them around).
For instance, I have a folder called "GCTs" in my codes folder. Inside of this folder are a bunch of subfolders named after what GCT is in it (Roy set, Brawl+ nightly set, Brawl+ official set, Ex Brawl set, ect, ect) with the corrosponding GCTs located in each folder. So when I want to switch sets, I go into the folders and copy/paste them into the root of the codes folder (overwritting the previous GCT)