I would say your best bet here if you have many multiple formats you’re working with is to create your edit you want. DO NOT RENDER ANYTHING YET.
Once you are happy with your edit you can go to media manager add a second or two handle so you can still make small tweaks, this will duplicate all your files without all the extra footage you’re not using.
Once you do this you then determine what your final output is? Is it 24p 1280 x 720 or something else? You decide at this stage. Then go to compressor and create your templates you want. You will probably have to create a new template for every type of format you are compressing from. For each output you want to compress to the exact sequence to which your new timeline is. I recommend creating tests for each new template about a second or so, this will save you lots of time if your template isn’t how you wanted.
That’s how I would do it, there might be better ways but it worked for me on my last film.