How to I transcode my complete collections to second mobile format in advance and pick right one?

Hi all, but confused by mobile sync, can you help?

I wish to keep all my collection in best quality on my Plex server, but have an external HD with lower quality versions of my movies to play on a mobile with limited storage. I wish to have all these done in advance to its not as slow when I want to sync something.

So my issues are:
I could you the built in system in Plex, but the settings options don’t seem to match up between the flex server and the flex iPhone app. I can optimise in PMS to mobile, but when i try syncing on my iPhone, it seems to do another transcode?

My other question is, can I just use Handbrake in advance to make smaller versions of all my movies? If so, how do I know that the iPhone app will sync the now smaller version.

Sorry if this is a silly question, but Ive not had much luck getting these to work. It either doesn’t sync to Mobile, or doesn’t play!
Thanks

Thanks, using a separate mobile library is actually a great idea.
I think it would be better to have these as versions in the main library but I don’t understand how that works