APL naming decides how to name APL files. Using the time stamp on the new file simply copies all the file times. After success you can leave the source file or delete or recycle. The option if the output exists decides if the file should be overwritten, renamed, or skipped. You can also have the file system build levels of directory so if you compress from Artist\Album folders you could keep the same by picking "2" levels. You can output to the same directory or choose a directory. Output options are things that change the output files. Showing the popups for external plugins decides if it should show or hide the popups used for external encoders. Playing a sound on completion is an option to make it a little easier to know the program has finished. The option to stop processing on an error will simply stop and not keep processing other files if an error or bad file is encountered. The option to auto-check on creation will verify any APE file as it is built. Modern APE files include the CRC of the whole file, so they can very rapidly check the validity. The Verify mode sets if you want to perform quick verifies or full verifies on APE files.
The processing priority sets if you want processing to be higher or lower than normal priority. Since modern computers are multi-core, this often makes sense. The number of simultaneous files sets the number of files to process at one time. Processing page has options that control processing. You can also pick from a list of external encoders in this list. The extra time that Extra High or Insane takes makes it not worth the couple percent smaller files. You can choose what compression level to compress at. Make APL (Ctrl+5) is to build APL files from CUE files to play individual APL files in your players. Convert (Ctrl+4) allows switching between formats. Verify (Ctrl+3) checks the APE files to make sure they're good. Decompress (Ctrl+2) allows decompressing APE, or any external format supported.
Compress (Ctrl+1) mode allows compression of WAV, AIFF, and SND files. You can pick the mode by selecting from the left-most box in the program. More about picking a mode and compression level are below. Use the program to compress, decompress, or convert your files.