Run...don't walk...to Premiere Pro CS6. It will mix frame sizes and frame rates properly, with no conversion necessary for nothing. It just does it.
FCP 6? Oy...looking at a lot of time and energy to get things just to a place where you can BEGIN editing. Converting all the footage to ProRes, converting all the footage to a uniform frame rate. And so it LOOKS GOOD.
FCP 6 is 5+ years old...really really old. Get something new that will handle this. If you want, you can get a free demo of CS6 for a month...if this will take less than a month, you are set. Also, you don't need to buy it outright. The Creative Cloud allows you to "rent" it on a monthly basis too.
This is complicated if you want to stay in fcp. I'm not sure how great a job premiere is gonna do (no matter what Shane says). Almost anything that automates the process is gonna limit your control and ability to get the best possible results.
I recemtly finished a feature doc with a variety of sources with different pixel dimensions and frame rates, letteboxed and 16:9 and 4:3 material. The whole thing had to be put in a 1080 24p timeline. It was then blown up to 2k and shown in a theater. I was amazed at how good it looked.
Here's some basic rules.
Compressor does a great job doing these conversions, but you're gonna need to customize your presets to get the best quality.
Prores is a great format. I recommend converting everything to prores.
If you've got material at for example, 24p (23.976 fps) and you don't mind if it's sped up a bit, conform it to 29.97 (if that's your target frame rate) using cinema tools. This just changes the speed at which the frames change, so no frames are added or subtracted. You can also do this in compressor at the same time you're converting to prores.
Make sure you turn on frame controls in the frame control panel and turn any applicable option to best. The timing options will also give you the ability to do the same thing as I described above or maintain the original duration. Again set the rate conversion to Best. If you need to convert interlaced footage to progressive, you also do it here. All these things can take a long time to do. Read up on qmaster to find out how to greatly increase your output speed in compressor. Also, you can set an in and out in the preview window to do a short test.
For scaling stuff, you use the geometry tab. This can be a little tricky to figure out. Doing short tests is the trick til you get what you want.
Post back if any of this isn't clear, or you need any further help.
What is your final deliverable? HD/SD DVD/web
I would either work in 1280x720 or 16x9 SD. 960x540 will only add more render time.
More than likely 1280x720 will suffice for all of these things.
Down scaling the 1920 to 1280 shouldn't be an issue.
As for the other SD source I wouldn't plan on it filling the screen.
Depending on how big it is to begin with and how much you scale it it will never look better in an HD timeline.
Scaling SD over 130% isn't going to add quality.
You may want to consider placing the SD video over a background or still. You could also us the same piece of video for the background part but have it fill the screen. You will want to treat it in some way by either adding a blur or color filter.
i used compressor to convert footage from mp4 to Apple prores 1024x576 16x9 and also change different frame rates to 25 fps
I resized all the big videos to 1024x576 and maintained the smaller videos like 640x360 in its original size as i will composite them together to maintain quality.
everything went well as compressor makes a very good job in resizing and frame rate coversion.
i noticed that compressor added at the head of the movies a white frame on most of the converted movies
and after importing the movies to fcp 6 i found that every time i use a movie with a white frame in the head Fcp crashes.
is it because of the frame rate as i noticed that the white frames are in the movies with for example 23.98 that were conformed to 25