Yes you can! You can launch it via the command line like this : mp3towave -C "pathtomp3"
Note that it needs the quotes around the path to the audio file and the c needs to be a capital C. Of course, the Audio Converter Pro executable directory must be in your path variable or you must put the explicit path to the executable in the command line call.
If you are converting to MP3, you'll need to specify the -3 flag.
-3 (Convert to MP3)
-C (Convert to WAV)
-M (Convert to WMA)
-G (Convert to OGG)
Syntax: mp3towave.exe -[3CMG] file