So i installed my ultra x3 800 watts psu today in my antec 1200 case,now the problem is instead of the fan facing up it is facing down in the case,will this cause a problem?reason it is like this is because the 24 pin connector would not reach through the back if i did not do it like this,

Not much of a problem if there is airflow around, but might suck in more Dust:)... And might hum a little extra notch
)

Depending on how close the fan intake is to the base of the case, it may hurt the fans performance a little.
Just run it for a bit a check you are getting reasonable airflow from the rear of the PSU and that it isn't getting too hot.