practicing intentionally speeding up and then slowing down is something i would avoid. something i dont agree with as your hands will learn to constantly change tempo instead of locking in at a variety of set tempos- as you would when you play a song.
i practice to a click for everything i do.
start slow, whatever tempo you can execute the rudiment continuously while staying relaxed.
set yourself an amount of time for each rudiment you're working on, then gradually raise the bpm after awhile(hours-days-as long as you need,ect) by maybe 4-5bpm. only up the bpm when you know you're comfortable to. raising the speed too soon will compromise the way things sound.
also yes, if you're going to play at different tempos, stop, make the metronome change, then continue on.
hope this helps.