Hi!
First of all, there are no "stupid" questions. We are all here to learn and I have certainly learned so much in the year that I have been a member of this forum.
I keep my fish in the tank when I do a water change--I feel that it would be too stressful to take them out.
I use a siphon hose and buckets to change 25% of the water (for me, that is 11 gallons). I use the siphon to "vacuum" the tank--I have no gravel, only a small amount of river rocks and I can easily see what needs to get vacuumed up.
The fish are big enough that I don't have to worry about them getting siphoned up.

They are used to me doing stuff in the tank since I do the changes at least once weekly.
There is no reason to change all the water (100%). As long as you vacuum the gravel and do partial water changes weekly, they tank will be fine. And of course good filtration is important.
If the gravel is really dirty, if it hasn't ever been vacuumed or it has been a really long time, only do a small amount at a time--the bacteria that build up in it can be deadly! It will really pollute the water.
What kind of goldies do you have?