First, find the center wire on each side (primary and secondary), pins 2 and 5, and cut the wire off close to the bobbin. Those are center taps, and they are not used. Your connection as stated shorts half of the primary and half the secondary. When you finish cutting, you now have a four wire transformer, with only pins 1&3 (primary) and 4&6 (secondary).
Pins 1 and 4 have the polarity marking dot in the maker's spec sheet, so connect those to the places in the schematic that have the dots - pin 1 on primary, pin 4 on secondary. This will keep the phase noninverting through the transformer.
The primary side is marked with a "P" as I remember.
