I routinely have a BUG but it is the same caliber as my EDC gun. Specifically, I carry a Kimber 1911 .45 ACP Pro Carry Stainless. My backup is a Kimber Ultra Carry 1911 .45 ACP. I also carry two spare mags so the mags are good for either gun.
The only change to my routine is if I am going to be in an area that is environmentally unfriendly to metal guns and 1911's, i.e. extremely wet and rainy or lots of blowing sand. For these situations I carry a H&K .45 USP Compact and my BUG is a G36. Again, both are the same caliber. Unfortunately they do not use a common magazine but at least I can rob cartridges from one magazine to feed the other. Granted, it would be better to have two guns that can feed from the same magazine but I can say, with confidence, that my H&K has never had a failure of any type so I do not see it as anything but a minor inconvenience.
I train with these four guns all the time and carry each in its respective holster in its respective place all the time.
May the Schwartz Be With You.