When the HD 300 is in stompbox mode, to go from one effect to another do you have to switch the first one off manually, or does it go off on it's own when you switch to a different effect?
quick answer is: yes.

you can only assign each FX block to one footswitch. you can, however, assign multiple fx to the same footswitch.

let's say i want an OD and chorus to come on at the same time i want a delay and reverb to go off. i would program them all to the same footswitch with respective pedals in the on/off position. however, with this setup i cannot use all the fx at the same time.

now let's say i put the od and chorus on a 2nd footswitch. now i can use them all at the same time, but i must hit two switches (turn one set on, one set off) when i don't want them all at the same time.