That's correct, you can set an adjustment for each of your lenses, up to a total of 20.
On both your bodies, it's the first generation type of MA....
- up to 20 lenses
- MA recognizes lens by model, not by serial number
- single adjustment for zooms
More recent cameras (5DIII, 6D, etc.) have a new version of MA
- up to 40 lenses
- camera recognizes lens by serial number, so you could have different adjustments for two different EF 50/1.4s, for example
- dual adjustments for zooms... one for the shortest focal length setting, the other for the longest.
I notice you hae 50/1.8... That particular lens is pretty widely considered not worth trying to MA. It's not consistent enough focusing from one try to the next, to be able to MA in any useful way. All your other lenses have better USM autofocus, are much more able to be dialed in with MA. WIth the zooms, you might have to find what MA they need at each extreme and, if it's different, set an average. Or if you tend to use the zoom mostly in one range or another, you could dial in MA specifically for that range and let the other fall where it will.
MA is sort of the icing on the cake, the last little bit of sharpness and focus refinement. You might have some other issues, either with the cameras and lenses or how you are using them. You might want to post some sample images with EXIF info, we could take a look and might be able to suggest some other things that would help.