When handling two versions of a dependency, it is very important that the author of that dependency is maintaining the same Form IDs across both versions. If they aren't, the two versions need to be handled as two completely separate mods.

Assuming that the Form IDs are consistent, as is the case for Classic Advanced Power Armor and most versions of the T-65, the following steps can be taken to handle updating both in lockstep:

1. Make your changes against a single version of the dependency (for example, always the ESL version)
2. When a change is ready to be committed, launch xEdit with these flags to allow for renaming of masters: -IKnowWhatImDoing -AllowMasterFilesEdit
3. Open your module and select the File Header in xEdit
4. In the Master Files section, right-click the MAST - FileName value (e.g. T65PA.esl) and rename it to the alternate master (e.g. T65PA.esp)
5. Select your module in the left tree hierarchy and press F5 to open the "Save as" dialogue box
6. Save the module to the Content directory of this mod to be committed
7. Change the MAST - FileName back for continued development (or reload xEdit, since you didn't save the changes)

Before releasing a new version of the mod, make sure to load up the alternate version that you saved alongside its dependency and check it for errors in xEdit. For example, if you develop against the ESL version of the T-65 mod, make sure to load the ESP version with the alternate version. This is essential to ensure that there aren't any Form IDs that have changed between the two. If xEdit does report an error with a missing Form ID or a Form ID that is of the wrong type, this should be reported to the mod author who created the ESP and ESL versions so that they can rectify it.