***How to use 5.1 and stereo on the same sequence and then export it properly?
You have to work in two Sequences:
- One with the Mix set to Stereo.

- One with the Mix set to 5.1.

The Track Mix option is set at the time that the Sequence is created. If you're currently working in a Seqeunce with a 5.1 Mix then copy and paste all of the Source Footage into a new Sequence set to Stereo Mix. Edit for Stereo as needed and then export.
When working with a 5.1 Mix, Output Assignments are set in the Audio Track Mixer panel.

If you happen to already have Linear PCM Stereo Stems and Linear PCM 5.1 Stems, those can be placed into a Multichannel Mix Seqeunce to export a main file that contains the picture and sound mix options in one file - but it doesn't sound like this is what you're trying to achieve.
***Also often need to combine several different frame rates for videos that have subtitles. I would be grateful if someone has a workflow for this as well.
It sounds like you're working with delivery files with Open Captions (the captions are always in view and cannot be turned off). Ideally you would have access to each Sequence that created those files such that you're working with textless source footage whose frame rate, frame size, and frame aspect ratio can be cleanly remastered, upconverted/downconverted, or reformatted as needed. If not the Sequences, Full Resolution exports without text (often called "textless"). Assuming that that's not the case, your quickest approach would be to use Content-aware Video Fill to remove the subtitles (the fill will be blurry) in After Effects and make sure you have Time Intetrpolation set to "Optical Flow" in Premiere Pro for any clip that has a frame rate that does not match the Sequence frame rate.


-Warren