Yes, when I used the experience system from Fifth Cycle I had the players note what they were 'working on' on the character sheet and describe when and how. No biggie.
And I agree that the ability to change the experience system and other parts of the game system without breaking it is one of the defining aspects, probably more so than the check system itself...but I usually use the check system myself. I have run many BRP games and only used the Fifth Cycle system once.