Apologies for my too-brief response, fmt3.
I should have said, "the thicker part of the eccentric should always be over the grub screws".
So long as you avoid the thinnest part, you should be fine. The reason for all this is the grub screws apply localized pressure and if this comes in the thin part, it can distort the eccentric.
Putting the thickest part if the eccentric at the 3 o'clock position is about the maximum, in my view. If more takeup is needed at that point, it is time to dial back the eccentric, remove a chain link and retension.
If you are reusing your present chain then you will want the eccentric in the position that allows you to properly tension the chain. I allow for 12.7mm or 1/2in of slack in one run of chain.
For reference, I've attached a couple photos of my Nomad's eccentric when I replaced the original Shimano outboard/external bearing BB with a Phil Wood unit.
As mentioned on the Forum previously, it is nice to align the grub screws with past divots they have created so as to avoid chewing up the eccentric unnecessarily. I can be helpful to invert the bike and remove the screws while using a flashlight to peer inside to see where past divots have come. If you enter the term "eccentric" (no quotes) into the Forum's search engine, you'll see a wealth of past information on proper settings wrt to positioning and chain tension. This topic is apropos to your situation:
http://thorncyclesforum.co.uk/index.php?topic=13038.msg97923#msg97923If you are fussy about saddle height and positioning as I am, you may also wish to readjust your seatpost and saddle at some point to compensate after adjusting your eccentric.
Best,
Dan.