Flaps essentially increase the wing size creating more lift.
Don't know what planes you are flying, but the planes that I fly the most (FM2 / F6F) ... the flaps do not increase the wing size ... they only change the shape of the wing which changes/increases the lift vector.
I use flaps whenever I deem them necessary ... going up or down ... it all depends upon the situation at hand.
I will use flaps in a spiral climb if needed.
At the top of a zoom, instead of dropping back down because the opponent isn't quite "roped" I will pop flaps, level out and float there a bit watching to see if he does stall out and then drop on him pulling flaps back in.
I will pop flaps out nose down (like Grizz) to pull the nose around or into my opponent quicker and once I like where I am at ... I pull them back in.
Once you get use to a plane and how it performs with flaps ... using them becomes second nature and you really don't even think about it anymore ... you just do it.