i have done a good number of gravel changes in my time. through trial and error i have found out what to do and what not to do.
as far as substrate, the best stuff for plants is somthing like seachem flourite, the standard version is a little rough if you have bottom feeders though. they do make a sand type though. regular sand is also nice and stays clean. as well as fine gravel. most of the packges say weather or not it will change your ph. but you might get spikes of different things or a bactira cloud just from stirring the tank up so much.
here is how i do it.
after taking all of the decorations and things out of the tank use a gravel vac to siphon out alot of the black gunk thats in the gravel. this will lessen the explosion of yuck into the water.
when scooping the gravel out i find that a plastic dust pan works best.
for putting the new substrate in a bowl works well for sand, just go slow so that it doesnt float around and get sucked into the impeller of your filter. for gravel the dust pan can be used again.
the water is probably going to be dirty no matter what you do, but it should settle out in a few hours. also, i take my fish out of the tanks when i do this kind of stuff.