That's correct.
If you think back to your days with apl's, you'll remember that to create one, you first have to specify a shapefile for which it pulls all of the schema from. Same goes for axf files.
While an axf file can hold all of your data, it can also hold your customizations. When someone is going to make customizations to an axf file for use each time they check out their data, I normally would recommend that they create that "template" axf file by checking out their data as "schema only". That way, it pulls the layer definitions (the stuff that is stored in an apl file) from the feature classes but not all of the data.
Any modifications are made within that schema-only axf file and it is then used as a template each time you check out your data. You would never actually collect any data with that file.
It's not really the best workflow to check out a single axf, check it back in, and then continue to collect more data within the same file (you can, but you can run into problems if your data is being modified in the office at the same time). I always recommend that you check out a NEW axf file for every new batch of field work. Each of these checkouts will pull the customizations from that modified "template" axf file which you have stored somewhere on your computer.
If you need to change the customizations in any way (such as adding a new field or changing the look and feel of the edit form) you can simply make changes to that original schema-only file. However, in the situation where you add a new field, it is easiest to just check out the feature class again (specifying the original custom form) so that you have a new axf file that has the new field structure, but the old customizations. That way when you go into ArcPad Studio to add the new field, you can easily select it from the drop down list as it sees it within the schema of the feature class which you've checked out.
I hope that makes sense.