I don't want to scratch the surface, and I want to get it back in smoothly.  I've never dealt with that type of seal before, any suggestions?  

Transmission, rear axle, year?  

I suppose that might be helpful

'69 351W, FMX w/9" rear end.  

FMX trans rear seal?? or rear axle seal??  

Transmission rear seal.

Not sure if the rear axle seals need to be replaced or not.  

Once you get the driveshaft out of the way it's not a major deal. After removal of the old seal, I personally, put a very fine coating of silicone around the metal part of the seal as an extra precaution against fluid getting by the seal body. There are seal installation tools available at most auto parts stores for rent, or blocks of wood, or large sockets, or just careful tapping around the perimeter to seat the new one fully. I hope this answers your question.
PS you'll know if you have a rear axle seal leaking by the tell-tale glistening seepage fron the seal area down the backing plates.  

With the vehicle being in a garage (not driven or started) for nearly 30 years would you replace it?  It feels very malleable, surprisingly.

Any tricks to get it out without damaging the mating surface?

Thanks!  

WPlayer,
If its not leaking leave it alone until it does. They make seal pullers to make these internal mounted seals removal easier. Some times you can put a sheet metal screw into the seal body and use it for leverage as well but it's a lot more work.