If you highlight a clip in the timeline and this clip is superimposed by another clip you will see no handles in the Program window. You need to highlight the clip in the Source Monitor, then the handles will appear.
Have you been filming Standard and Widescreen on the same tape.
Widescreen is anamorfic which means it will present itself in 4:3 vertical stretched in a Standard project.
If its for Premiere Pro i would use neither.
You want an intermediate file not a compressed one like mpeg, as you are going to export again.
Use uncompressed or Lagarith or even Cinefom.
Proxies sound good but if you still have to export with the original footage to final destination on the same machine, you are back to square one.
Might want to have a look at NeoScene from Cineform. https://www.cineform.com/neoscene/