The thing is, the png format is what gives you a transparent backround. If you convert your pngs to jpgs they will all have solid white backrounds and be pretty much useless for scrapping. You could always just do it in Windows but again then they'll have white backrounds.
I would think your program would recognize pngs. Will it let you bring anything in? If it's proprietary it may not let you use anything other then what is supplied with the program.