I do a circular route that is basically running up a steep hill and back down - 3 miles length. Now if I do it clock wise this means a very short (0.8 miles) but very steep climb to the top of the hill followed by a long (2.2 miles) but more gradual decline back to the start. If I do it anti-clockwise I have the gradual long incline followed by the steep short decline.

Which is the best way of the two and which should be fastest and why?

Depends on your build, to a large extent !

I'm carrying a bit of surplus weight. Long slow grinds up hills really take it out of me compared to short sharp climbs.

Also, a long gentle descnet I can really punch out the pace (for me) at sub-8 min per mile. A steeper downhill can actually be harder to run quickly, as you may tend to lean back and 'brake' if it's on the edge of your comfort zone.

One of my runs is a similar sort of thing to what you describe. 5.5 miles.

I can either do 2 miles of really hard work (800 feet of climb), followed by 3.5 miles of drop. My PB for it is a few seconds under an hour.

The reverse route - 3.5 miles of more gradual climb, followed by 2 miles of drop (and 1 mile of it is pretty steep drop), I can't break 1:05 for