You can log directly to the SD card, and should do whether you are sending direct to NMEA or not. The format will be ADM, which is only readable with "Homeport". You will then need to export the data from homeport into a format that retains the depth values. I'd suggest csv as it gives you the opportunity to remove dodgy data in excel before chucking it at RM to do its business on. You'll be able to make charts for your 541s as well.
Trevor