Project using several MP4 elements vs hundreds of MOV and JPG's

I have Adobe Premier Elements 14.  I am working on a big project that will integrate numerous  video clips (mov files ) and still pictures (jpg).  To simplify file management I was thinking  of  generating several sub projects with PSE14 and creating MP4 files based on grouping subset of jpg's based on common criteria like day or city visited.  Also do the same with groupings of video files.  Each mp4 in turn would have its own custom duration, transitions, background music and titles.   The main benefit is to make editing simpler and avoid major mistakes that might render a complicated project hopelessly unrecoverable if I make editing mistakes.    My consolidated project will just be a succession of a dozen or so elements (mp4 clips), DVD menu and opening/closing titles.  My main concern is that I will lose significant video quality in the final project vs if I created from all the hundreds of elements.  Is that likely?  All elements were taken from 2 cameras:  Iphone SE or a Canon Sureshot D20 (for the underwater pics) which are lower res than the Iphone. I will be taking the final PSE14 project and creating  ISO files for both  DVD and AVCHD disks with settings for max quality.

Your help most appreciated.

PS  I am assuming I can't integrate multiple  PSE14 level projects in their working form, which would be wonderful.