It's been a while since I've used traces as sources, so I haven't been observing how well they fit recent imagery (but I'm sure it's much better than it used to be). Personally, I would say that if you observe a consistent overall offset for a given trace, it would make sense to retain it, or at least split the difference, with the understanding that future imagery might very well fall in line. Of course, in areas already densely populated with features, you should generally align with those, as already discussed.

Hopefully the imagery alignment will continue to improve, but for now it's a good idea to keep an eye on its overall fit to the part of the map you're working on, and account for that. This is doubly true when using some of the other available backgrounds, but they can still be useful for seeing a differently lit view of a shaded area, etc... just take the geo accuracy with an extra grain of salt. I'm not aware of anything better than the default Bing imagery being readily available, but if you find something, let me know!

(BTW, last I checked, the custom background feature in ID wasn't retained across logins, so if you set something up, keep the info somewhere handy so you can paste it in again if you need to.)