1. An alternative to two tenons butting in the middle of the post is to make an over and under tenon. This way they can be full length and have plenty of wood left for the pin diameter problem you are facing.
2. round pins are easier to bore a hole. square pins would require more work to make exact sizes.
3. You can center the tenons if you want to, but you need to consider the layout on both pieces, so that they align properly.
We use a method called "square rule" where you layout by using a standard framing square and offset the tenon by either leg of the framing square that way the layout is the same on both pieces as you use the same tool to layout both.
And you need to consider the amount of wood between the mortise in the beam and then end of the beam. It is usually stronger to leave some small section of wood between the mortise and the end of the beam so you wouldn't have a open mortise on the end.

There are good views of joint in the pdf files available from the guild website for free download.
Look for the Historic American Joinery series and you can view different joints, together and exploded to see how timbers can be joined.

Good luck and keep asking questions.

Jim Rogers
PS see over and under tenon example in my avatar, to the left.

Last edited by Jim Rogers; 05/20/12 12:41 PM. Reason: add ps

Whatever you do, have fun doing it!