You've got a few choices:
Plan A:
You can either discard the 29.97 footage completely from the main project and stick to the 50/60 you have.
That way you won't have a video which changes quality every other clip or so.
You could keep those bits for later as a 'special feature' section on the disk.
Plan B:
Your lowest frame rate is 29.97 (NTSC) so base everything on this rate if you want to include this lower rate footage.
(Ideally you're thinking of 25fps if you're in the UK to be compatible with BD (Blueray) players, unless your audience has multi-region players but don't gamble on it).
Space on BD disk permitting, you could then have a 'special features' bit that shows just the exciting parts of 60/50 footage.
With a mixed bag of frame rates, use the lowest common denominator (in your case 29.97 but actually working at 25 because of your region). If, as you say, the quality is much better at 60, you can't UP the quality of footage that came from a lower rate (29.97) but you can always bring the footage with higher rates down (60 and 50 -> 29.97).
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Each project is different.
If you can stick all your footage on a single disk at 25Mb/s that's great but be prepared to
either sacrifice that down to 18 or much lower
or make your film shorter to maintain image quality if your intention is to fit it all on a single disk.
To start with, try the settings that PD has as default.
Use this as your starting point.
Check this against the Blueray disk space available.
Tweak up the settings but stick with MPEG2 (IMO) or test with H264 until you start to notice those gremlins.
If you have a high end burner that can burn high capacity BD disks just make sure that your high capacity BD disk will play on a normal player. Not all players can read those high capacity disks, so stick to the lowest common denominator. You are working with big files. Just remember that to maintain image quality, use very little compression and keep the bit rates up.
It is a juggling act.
This message was edited 2 times. Last update was at Mar 21. 2014 05:47