Is it OK to rename your MTS files once you've transferred them to your computer? Like mountains1.MTS, mountains2.MTS, etc. Seems like it would make it easier to find in the future. Or is it better to just rename the folder containing the MTS files?

Whatever capture program you are using should be able to for this for you. If I were to use PPro and use a batch capture I could specify each starting file name ("Name001.mts or date.35.mts) whatever you want. I dont use this I use HDV split which allows the same naming procedure. I would think this should be a standard feature of any software. Check your setup screens carefully before capturing.

Its OK to change the names of the footage as long as its before you put them into an NLE.

If you do it after putting them into a project the project will complain that it can't find the
files...

best to do the renaming during the capture .... use split scene option if you want to get
separated files...

Thanks. I'm using memory cards so no more capturing. Just file transfer. I know with the capture window in PP I would name the file there. I like these memory cards (HF-S100). Just pop in the card and move/copy to where ever.