This may be a really easy thing to answer, but I'm a little stuck-
I have a sequence that I need to send to color, but unfortunately Ive had to use some trickery to cover certain things up in the shots tiffs with alpha of a bit of wall to cover up another bit of wall which had a screw in it, that sort of thing). This means that if I send it as it is, I will end up with a color corrected sequence but with lots of patches of wall which haven't been color corrected, because of color's inability to color certain gfx files. The most simple thing I could think of is to export a quick time mov, reimport that into a sequence so its all one track and then just add cuts where I need to have different color grades, but that's a bit of a pain with the amount of vids id need to do it with.
In photoshop I would be able to merge a bunch of layers in order to apply one filter to what used to be 3 layers ( I know they're totally different applications with a totally different set of rules, just trying to give an example of the sort of thing I need to be able to do). Is there a way to do something like this in FCP to specific parts of the sequence?
sort of yes, but really your first suggestion is the way to go.
you can NEST the fix-up shots, but i don't think colour will see the nests as one item.
good thing about nesting is you get an instance of the nest in your browser,
so your fix shots are ready for batch exporting.
they still need to be placed back in the sequence (or a copy of it)
Don't nest. Nick is right, you need to make a new quicktime of your composites. Boring but it works. I sometimes do layers with mattes and you can paste the grade from the top track to the stack underneath but tiffs (still frames in general) are no good in Color.