I was planning on changing out the 2-3 inches of bare gravel for something like flourite and then putting another thin layer on top of the flourite. whats the best way to go about doing this? put the fish and plants into a bucket, remove all the water, do the change, fill up partially, plant, fill all the way, add fish? how can I minimize stress for the fish? is there anything else i should know before i start?

That would be the quickest way to do it. Just make sure you put the filter into a bucket to keep the media wet. Keep the fish in a dark place to keep the stress down. Before you start pulling out the fish and plants make sure you have the new substrate ready (rinsed and all) that way it will go faster.