I'll answer the bit I do know about, but I don't know how you've got the emulater set up, so I cannot say a lot about that.
You'll need to LOAD the BASIC code back into Loco BASIC, and then resave it as ASC which is normally:
SAVE "PROG.TXT",A
If you don't put the extension in, the file will be saved as .BAS which might overwrite your actual .BAS file, which you may not want. The ,A on the end forces the save as ASC (i.e. plain text) rather than the encoded (tokenised) BASIC.
Then, you need to put the file somewhere that you can get at it when you come out of WinApe, and that will depend on how things are set up, and what you want to do with it later.
Geoff