Hi,
Here's what I would recommend:
Get one of your AXF files looking / behaving exactly how you like it.
Next time you go to check out, on the screen where you are selecting the different options for the layers (Check out for disconnected editing / background layer / etc) there is a white checkbox on the right side of the window. If you click it, it'll open a browse interface.
Browse to the .AXF file with the forms / scripts all set up how you like it, open it, and it will then open another window where you'll select (from within the AXF you just selected) the layer whose forms you want to use.
So for instance, if you have five layers you want to do disconnected editing on, and modify 5 layers' forms in the AXF file, you'd see five layers listed. Just match them up with the appropriate layer as you use the check boxes. This will force the forms / scripts you use in the "customized" AXF file to be used on those layers every time. The checkout process will remember the AXF you specified, and always use those forms until you change it.
Good luck!