I have a flip flop hub with 16t on both sides fixed and freewheel. I want to put a 18t freewheel on one side is that too much of a difference? would I have too increase my chain length?

It depends on a few things. How long are your dropouts or track ends? How far forward is your wheel in that dropout or track end. You can always purchase a cheap chain and have it as a back up if you don't need the new length.

Post a picture of your dropouts/track ends. It should be easy to determine from that.

You would need to see a little more than that. How far back his axle sits when the chain is tight with the current xx/16 ratio would need to be shown, not just the dropouts. And even then It would be hard to tell from a picture if it would fit or not for sure, unless there is a drastic amount of space available.

Oops, that's what I meant. I should've been more specific.

It depends on your dropouts and chain length. Unable to determine given limited information.

I'm told that each tooth needs another 1/8" in a track-end, so if you want to add 2 teeth, and you have track-ends, you should be good to go if your current 16t can be moved forward a quarter inch.

What this guy said.