I think the problem is that people are looking at, say, rock, and cut-stone, and seeing TWO seperate piles: The basic rocks, and seperately, rocks that have already been converted to cut-stone.
This though, is not how it works.
It's better to think of it as: The first number is the amount of actual rocks you have, and the second is the amount of POTENTIAL cut-stone that you can use based on how many rocks you have. So, with the mason's 3:1 ratio, if you were to have exactly 3 rocks... no more, no less.... the game would list your cut-stone amount as being exactly 1, because that's the amount of cutstone you can make with the 3 rocks.
If you're having trouble getting enough of a resource like that, be it the cutstone or lumber or whatever, you dont need to do anything funky with the mason or the carpenter or whatever; simply work towards getting more of the basic resource, because that's the number that counts. Placing down more masons or whatever wont do anything at all. There's no per-turn conversion speed or anything.
....and the other problem is that the concept is just kinda screwy to explain. I keep trying to think of a really good way to explain it, and I keep not managing to actually do so. One way or another though, it seems to be a constant source of confusion among new players, that's for sure. I remember the first time I played it, I was baffled by it as well.