About Thermal Pads and usage of Heatgun?

I have a CECHA01 ps3 60gb. and I wanted to know if removing those annoying peach colored squares that are thermal pads (I'm guessing) was a good or bad idea. Since they were dirty as heck like the others. I'm getting my kit soon, is why I asked, thanks for reading this. in some cases the patch (NOT the 2 big black pads) but the big peach ones are located underneath the Bluray reader drive and on the motherboard for another component. could someone please explain what those both go to, and if i screwed up by removing them?

Also, if anyone can help me understand the heat gun's usage and every possible thing that a total dummy would need to know, I'd be very grateful since I only know it pumps out either "low" 500F to "high" 1000F heat, and DO NOT want to ruin my motherboard, so any video guides regarding this procedure would be helpful.(the one on this site sucks) and details entailing handling the heat gun, how long it should,or shouldn't be on for, etc. the stuff i have no knowledge about with the heatgun.