I recently ran 12-3 wire off a 15 amp breaker as a main feed for my 2nd floor, only problem is it connects to 14-3 at the closest junction box to spread out to all the other connections on the 2nd floor. Is this okay? Also I prob. Only had to run 12-2 anyway as there is no other connection between the circuit breaker and the junction box...

It all depends on what the 14/3 feeds. If it splits off into two circuits then yes, you did good by running 3-wire.
How did you hook it up in the panel? Did you splice it wire for wire in the junction box?
Who ran the 14/3 and where does it go?

You should not have run #12, or should I say you did not have to. MAKE SURE you keep it on a 15A breaker. I would out a label on the wire in the panel and mark it "15A ONLY". This way no one later will see a #12 wire and put it on a 20A as is typical.

If anything you have overkill. You might save this Wire sizes, gauges, for breakers (http://www.greatinspector.com/faq-elec-wiresize.html)

Thanks guys! I just wanted to make sure it wasn't a fire hazard, someone had told me the only thing is the 12-3 wire might run hot and send spikes threw the current, also the junction box I ran the 12-3 into had multiple circuits coming out of it so I figure now that the 12-3 was needed. Im so far ahead after drywalling the 12-3 into the ceiling that it would be eaisier for me to replace the 14 gauge wire now instead of redoing the 12. Also to answer stan I made a short cut down at the panel by tapping the 12 into the 14 that origanlly came out of the panel... kind of rigged right now but I was not comfortable just yet with making connections directly into the panel. That will come later.

If anything you have overkill. You might save this Wire sizes, gauges, for breakers (http://www.greatinspector.com/faq-elec-wiresize.html)

I agree!

I also agree with Stan, make sure you label the wire at the panel.