Being a recent convert i can confirm that 64 bit is definitely the way forward
As long as processor supports 64bit then you should find transition relatively simple... at least i sure did, especially since you are starting from scratch with a clean install.
In terms of the downloads i can't see why they would restrict this. As the boxed version comes with both versions i'm sure they would offer the same facility for downloads. I am pretty sure the restriction would be around the key only, not number of times downloaded.
You might download and then lose the install file before installing. Not on to say, "well tough you can't have the product you have bought now". So as i say mostly likely both built into the one download, or able to access both and only prod key is the differentiator.
If that makes sense...