I'm also using the Spin Doctor truing stand. You really need to buy the alignment tool, which is essentially a plastic triangle with two bolts at the ends of one edge to engage the fork-ends of the truing stand. The alignment tool allows you to center the notched gauge (for lack of a better description) within the truing stand. It's not all that precise, but you should be able to get the rim centered within about 1mm using the little notches as a guide. I think the alignment tool is about $8, as I recall.
As for your rear wheel tension, assuming you aren't using a track hub, then your spoke tension will be much greater on the drive side then on the non-drive side. I believer Gerd Schraner recommends about 225-250 lbs on the drive side, and about 165 lbs on the non-drive side, for your typical box-style rim (Open Pro, etc.).
Tensioning the rear wheel takes a bit of trial and error. You need to tension the drive side first, pulling the rim far to the right, before tensioning up the non-drive side. It doesn't take a lot of tension to pull the rim to the left, because the spoke angle on the non-drive side gives more of a mechanical advantage for moving the rim than does the right side.