Here's the 'source' for my one if you haven't seen it: https://dl.dropboxusercontent.com/u/13905750/code/flickflag/index.html?p=8fdcad568be900e3ed4e8a54a6f5c03f

The third row of 16 boxes, below the palette and the frame number allocations, allows you to set flags A-E on. So if you put A in the box below red, clicking red will mean that A is on from now on.

The row of 5 boxes right at the bottom will go to a different frame depending on what flags are on. In my game, the first box on frame 1 is marked 'go to 14'. That means that once flag A is on, the game will always load frame 14 instead of frame 1 whenever it's directed to frame 1.

Earlier letters appear to take precedent over latter ones. So it will check for A first, and if that's on it will go straight to the frame in the first box and not check the rest. But if it's off, it will move onto the next flag check (B). As far as I know, there's no way to turn flags off again after turning them on.