A flex position is where you can have an extra regular roster spot. In most cases, its a WR or RB position, but some leagues use a WR or TE flex position.
Its basically allowing you to start an extra player, so you need to take a look at your scoring to decide what player would fit best. If the flex spot is WR/RB and your scoring system favors runningbacks, put your 3rd RB in that starting spot. If your league favors wide recievers, then plug in your WR there.
If the flex spot is WR/TE, you will fill it with an extra WR, unless you have 2 top notch TEs.
Hope this helps