I recently bought a 44cm mercier kilo tt. mercier runs big so really its about a 47cm. anyways, i'm kind of getting used to it but it still feels big. the standover feels tall for me. the wheels are 700c also. for more comfort on my bike, should i get a smaller frame or 650c wheels?

Well, standover should never be how you "measure" a bike. If you can get a foot down with one foot on a pedal you're ok in that respect.

Going to 650c wheels will lower the top tube, it will also reduce cornering clearance. If you're riding fixed, that's a VERY big concern. (pedal strike on a fixed gear more often than not involves you meeting pavement)

I just looked up the geometry on the kilo TT. Wow, it's long. 503mm top tube. Heck my 50cm SST-AL is 515. Then again, that's not what you're complaining about. Sounds like you've got some remarkably short legs there buddy :-)

If the rest of the bike fits, I'd say suck it up. Track bikes by nature are taller than your typical road bike, as they require higher BB heights, so you're getting what you asked for. :-)

If a bike doesn't feel right, you won't ride it. Frames that small really deserve 650c wheels. I'd sell that bike and keep looking.

Based on your questions I would suggest going to a Local bike shop. Might have saved you some money had you done this from the start. Get it fit even if you have to pay for the service. If you/they can't get it to fit proper..... Sell and move on.

If they wanted a track bike, a LBS may not have been the proper option. I went to seven LBS's looking for a track bike, and ended up needing to special order a bike. That said, our customer here probally "knew what they wanted" more than they really knew what they needed. It sound like the OP bought on hype, rather than need. :-)

I agree, head to the LBS, figure out what works.