Hi! The file selector starts from the location specified with Dir$. Looking at the amos sources I see that the default Dir$ path loaded during startup can be chosen in the amos interpreter config following these steps:
1. Make a copy of your current AMOS interpreter config before making any changes (on my computer it's located at System:S/AMOSPro_Interpreter_Config).
2. Open "Set Interpreter" from the dropdown menu in amos, load default config, and click on the last button on the list. Change the path in the first text box and save config.
3. Try copying things from APSystem to your source path until amos finds everything it is looking for, or give up and revert the interpreter config to the backup you made in step 1.
Thus it is possible but not as simple as it easily could have been.
There is another thing you could try out instead of changing the default path, if you haven't already: there is an option in the interpreter config for enabling auto-resume. That's what I use, and it works well except each time a program crashes the computer (..which of course could happen quite a few times in a row when it first gets started).