I have two different kinds of pellets and a third is on its way in the mail, plus frozen bloodworms and frozen daphnia and freeze-dried bloodworms. Also two nets, but I found the less stressful way of getting them out is to scoop them out with a cup. Lot of times, the suction of the cup draws them in and you just have to act quickly to get the cup out of the water before they swim out. Uhm, spare plants, spare hiding holes (in the form of clean PVC pipe), extra heaters . . . nope, you're not being over-protective at all. You're being a betta owner.
Did the pet store employee tell you how to suck the detritus out from the gravel? Same thing with the marbles, you'll want to use the hose to suck all the poo and uneaten food out from between the marbles.
Only time you'll upset Ahto is when you fast him. Some bettas will sulk during fast day. Mine bit me and then hid for the day in his little cave. He also bit me, twice, after I sucked him up the hose.