You boot from the USB just like you boot from the CD.
Try going to the BIOS setup and changing the boot order there. (Need to hit some key early in the boot to get there, the key depends on your hardware, could be F10 or F1 or del or... It's likely advertised for a short while on screen.) You might have a buggy BIOS, those are 13 in a dozen. Then save the settings and reboot with the CD or USB inserted.
Some people find the transition to Trisquel to be very easy, some might find it hard. I would guess it largely depends on one's experience and motivation. This weirdness you're currently enjoying with booting has nothing to do with Trisquel since you haven't even booted it yet.
