Maybe a dumb question but here goes. I have my engine and manual gearbox both out of the car. I drained the oil from both and replaced the output oil seal on the box. While it was standing upright whatever oil was left in it came out onto the floor. I realize upright isn't the normal position for it but is there a gasket that needs to be replaced or will it be okay back in the car horizontal?

 

Any seal has a holdpoint beyond which it will leak. Sounds like standing upright exceeded yours.

 

There is also a vent on the top of the gearbox, did the oil drain from that?

 

Was the gearbox standing with the bell-housing end resting on the floor ? If so, there is a seal at the clutch end of the box too. This will not withstand constant oil presence, and anyway, will be worn the same as the seal at the output shaft end. Best to replace all seals if you've got the engine and gearbox out of the car.