You seem to have two different questions, somewhat vaguely asked. I'll attempt to address both the questions I see:
The "soldier course" is the rectangular blocks that "stand" on their short end to make the border. The all go in one direction along each edge, no matter what the field pattern is. A quick DuckDuckGo search for "paver soldier course" got me this image:
Source: Western Interlock. No endorsement intended or implied
I'd suggest that you'll want to start with the soldier course of 6x9s to outline your paver area, then lay the field.
You'll need to measure (or do a test layout along each edge) to see if you need to cut any blocks at any of the borders. If you do, figure out where to best put the cut edge (where it's least visible and annoying). If you do the field first, then get to the soldier course, you may discover that you need to cut the soldiers and that will look odd. Of course, you may be able to extend the pavered area just slightly to avoid any cuts, and, if you need to have a row containing a series of less than half blocks (long way), you may be better off expanding or contracting the area to avoid those cuts.
I was thinking if I lay just the I's (6x9) all the way down, that's two pavers horizontal and two vertical, then come back and fill the spaces with the 6x6 blocks, it should work.
Based on this description, I believe you're doing this "I" pattern:
Source: Angelus Paving Stones No endorsement intended or implied
I believe you can, in that case, lay out all the 6x9 blocks, then go back and drop the 6x6 in the holes. However, you may discover that keeping them lined up nice and straight with all those holes gets to be difficult. It also increases the chance of someone knocking pavers around when moving on the partially laid surface. I'd suggest that putting the 6x6 in as you go will help hold everything in place and ensure that you maintain your straight lines and help provide a professional looking finished job.