For your first issue, it sounds like the files were moved before the option to also move non-media files was checked. Correct? In this case move them manually.
If they are missing tags, they cannot be automatically organized. Drag and drop them into the MB inbox, right-click on the tracks to edit the tags.
Home Desk ~ MB 3.3 Portable • Questyle CMA400i (ASIO) • Sennheiser HD 660S (balanced) / Audeze EL-8 Closed Back / Fostex TR-X00 Ebony • Teac AI-101DA • Jamo C93 + Dayton Audio SUB-1000
Work Desk ~ MB 3.3 Portable / Tidal • SMSL SU-8 v2 • Nobsound NS-05P • THX AAA 789 • Sennheiser HD 58X (balanced)
OTG ~ FiiO M11 • Audiofly AF180 / B&O H6