To format a USB you should find the info on your machine under the Settings tab. Open it and look at the Embroidery settings. You may have to change pages to find the Format area. Put a blank USB stick in the machine before you turn it on. Then find Settings, Embroidery, Format. This should be in your owners manual also so look at the Settings info probably near the front of the book. I am not where I can look at a manual. Sorry.
Yes, it you format a USB that has designs on it, you lose them so be sure you have them stored elsewhere. When the USB is formatted, it puts a folder on it where the machine looks for designs and where you will copy/paste them to from your computer. Only put copies of designs on the USB. Only use a 2gb or less stick. Anything outside the folder will not be "seen" by the machine. The machine looks at ALL the designs in the folder when you first open it on the machine. The more designs you have on the stick, the longer it takes to open and let you find what you are after. So that is why you should only put a few at a time in the USBs folder. Stitch them, or remove them... Then put other designs on it.
Hope this helps. I am not sure how the WiFi features work. Maybe someone else can help with that. Reading your manual is also a good idea and there is help on the Janome website under the Learning tab if you don't see info here.
Tracy in Nashville, TN
Martha Pullen Licensed Educator