Changing from a racing double to a compact double is a smart move. Most riders have very little use for a 53-12 compared to the practical value of lower climbing gears. I'm even building up a bike with a "sub-compact" double - 42/26 or 42/28.

What kind of crankset and BB does your bike currently have? Cranksets can use different bottom brackets to get proper road chainline. This is especially true in the square taper world.
But if your current BB puts the new crank in the proper positioning, and bearings still are smooth, I'd stick with the old BB. The bearings wearing out won't damage the bike, whether in a cartridge unit (square taper or Octalink/splined) or external-bearings.