David. Sorry, my apologies.
I scoured the 'net for hours searching for a good pic of what I mean. There's not much out there for pics unfortunately, but this one is about as close as I could find:
View attachment 68890
It's very similar to what you mentioned, you want to have your cuts offset from each other on the same pillar, and have overlap to plug weld into if possible.
In the photo above, they were able to do it at a factory overlap point. You might get lucky and be able to do that too on your "A" pillars if the ones on your Malibu are anything like the ones on my Cutlass:
View attachment 68891
The "B" and "C" pillars may be a different story tho, as there's no obvious overlap joint to separate them at:
View attachment 68892
Again, I know it's on my Cutlass, and not on a Malibu, but the same principle still applies. Don't cut all the way through in a straight line. Stagger the cuts whenever possible. This adds strength and maintains the structure.
I would invest in a high quality spot weld cutter, and try to separate the pieces where the factory assembled them.
The first photo above was borrowed from NastyZ28.com, where they replaced a roof on a Camaro. It may be of some assistance.
http://nastyz28.com/threads/roof-replacement-fisher-t-tops.213257/
Hope this helps a bit. Good luck!