I would always say break your kit down as similar to the other post you can find yourself not being able to seperate them at all!
I have a Sea&Sea housing for a D70 and even on a weeks diving holiday have had problems seperating a compact flat port from its extension ring, so now every couple of days I seperate them and clean and re-grease.
I bought the housing second hand and the previous owner had left the main body o-ring in the housing while storing it, the o-ring had taken the shape of the housing and was effectively useless.
I'm afraid you just have to be completely geeky about it, break stuff down so it doesn't get the opportunity to seal permantly and always when storing kit remove the o-rings.
If possible have a couple sets of o-rings and rotate them, when not in use clean them and put them in your every trusty zip lock bags with the o-ring name and number, ie Main-1, Port-1.....