The most important thing is to kick the filter with your fingers in the first runs to purge it. Once it is purged and all air bubbles are out, it does not matter orientation, because fuel flow does not have enough speed to cavitate and generate new airbubbles.

Once the line is completely purged, you rae free to go....

Perhaps there might be a microscope leak in your fuel filter. Put it under water and test it for leaks

Regards

Nuno