It all has to do with qualifying times. The top 6 highest qualifiers that transfer through their heat race line up in the top 6 spots of the feature, inverted.
For example, last night at Kokomo:
QUALIFICATIONS:
1. Hunter Schuerenberg, 35, Byram-12.675 - (Did not transfer)
2. Justin Grant, 40, Grant-12.788 - (Transferred)
3. Jerry Coons Jr., 71p, Phillips-12.792 - (Did not transfer)
4. Dave Darland, 21x, Roberts/Tate-12.838 - (Did not transfer)
5. Daron Clayton, 69, Dynamics-12.841 - (Did not transfer)
6. Shane Cottle, 11, Walker-12.889 - (Did not transfer)
7. Mike Spencer, 50, Chaffin-12.953 - (Transferred)
8. Chris Windom, 5x, Baldwin-13.001 - (Transferred)
9. Jon Stanbrough, 53, Fox-13.016 - (Transferred)
10. Casey Riggs, 37, Indiana Underground-13.041 - (Transferred)
11. Andrew Elson, 27a, Elson-13.045 - (Did not transfer)
12. Chad Boespflug, 98x, Gatt-13.063 - (Transferred)
The cars in bold transferred to the A-Main and lined up inverted in the top 6 positions like this:
Row 1: 98x Boespflug - 37 Riggs
Row 2: 53 Stanbrough - 5x Windom
Row 3: 50 Spencer - 40 Grant
From there, the rest who transferred through the heats and B-Main line up straight-up behind the first three rows according to qualifying times like this:
Row 4: 35 Scheurenberg - 71p Coons
Row 5: 21x Darland - 11 Cottle
etc., etc...
Out of the top 12 qualifiers listed above, Clayton and Elson did not make the feature so were not included.
Hopefully this cleared it up a little bit.