MIPS R4000 was SGIs first 64-bit processor and was released in 1991 and first used in 1993. The first 64-bit version of IRIX (version 6.0.1) wasn't until the end of 1994 but was limited to only a few higher end systems. The first 64-bit version for all major systems was 6.2 and was released in March of 1996 (and happens to be the version I'm using).
In the almost three years from the first 64-bit processor system to the first major 64-bit operating system, SGI was able to make sure that 6.2 was binary compatible with IRIX 5.3 (the previous major OS version which was 32-bit).
If Apple makes a transition, I would expect no less a smooth transition. On my 64-bit OS I run 32-bit and 64-bit apps side by side seamlessly. For example, if I didn't know that both Photoshop 3.0 and Illustrator 5.5 were 32-bit, I couldn't tell by how they run on my system.
I don't know if Apple has two versions... I wouldn't think that would be needed at this point, it is making sure that current 32-bit apps don't suffer from the move is what Apple should be working on. If they do, I would expect that a 64-bit version of Mac OS X Server would come first.