Using Serial monitor on Adalogger M0 w/ SAMD21

I seem to be having trouble accessing the serial monitor while a sketch is running using the Adafruit Adalogger M0 with a SAMD21 chip. From what I've read in the tutorial the most recent board versions available via the boards manager don't require much to be changed to access the serial port. But as I found out here https://forums.adafruit.com/viewtopic.php?f=22&t=98197&p=492182#p492182 I seem to have changed something on the board that requires putting it in bootloader mode just to upload a sketch, and being on a different port while in bootlaoder mode it makes things even harder. So I'm not sure what I messed up to require the bootloader mode, hopefully fixing that will fix the problems with accessing the serial port.