Can someone tell me how to take pictures?

I'm having problems using my "new" meduim format SLR. I'm almost certain the problem lies with me, not the equipment. The issues I mention are diminishing the more I use the camera, but it's time I asked for advice. I'm running out of expired film so need to speed-up my learning curve.
Yes, I have also used fresh film, and my problems (when present) are the same.

I'm using a Bronica GS-1 purchased off ebay. AE finder, 100mm lens, and a handful of backs. My main camera is a 35mm Sears KS-2 (rebranded Ricoh XR-7). I'm having difficulty switching between the Sears and Bronica.
If I spend an inordinate amount of time to take one picture using a tripod there are no problems. I am sure I'm not accounting for the differences between the format size, lens size, and quality of the cameras.

Part of the problem is I traditionally take snapshots. I tend to use small apertures to bring everything in focus, aperture priority to let the camera think for me, and wide-angle lenses to get a wide field of view (which I know is not how I'm "supposed" to use them). I'm sure I'm not using the Sears "correctly," but it doesn't seem to matter with snapshots. Yep - 80% of the time I pretend my 35mm is a point-and-shoot. If I use the Bronica this way I don't have many problems.

As I try to improve my photography, the Bronica is giving me issues and the Sears is not; my 35mm photos improve and MF degrade.

When comparing the cameras, I use the 50mm lens on the Sears. Each camera's focusing screen has both split-screen and micro-prism ring.

I'm having difficulty focusing on what I want at wide open aperture - the photos have shown a focus other than I thought. When present, the error is in different directions (before or behind) on different photos, with the subject the same distance, so I think it is me and not the camera/lens. If I try hard enough I can get what I want - but it is a lot of work.
On my 35mm I usually ignore the micro-prism ring and focus with the split-screen, which is at a diagonal. Typically, I'll find a straight line to use it on even if it is not exactly at the distance I want to focus. This is usually fine even at f2.8.
The Bronica's focusing screen does not seem as distinct. Also, the split-screen is horizontal, which I find a bit more difficult on any camera I've used. If I use it as I do on the Sears, I can have problems at wide apertures.
When I use the micro-prism ring I generally have fewer issues, but it is thinner than the 35mm and not nearly as easy to see.
Would a different screen (or optic) make a difference? Is it common practice to stop-down when hand-holding one of these cameras?

Again, I don't have to think much to use my 35mm. The Bronica, on the other hand, seems to have much more "accurate" metering. It is fine in consistent light, but in mixed situations (e.g. dappled sunlight under trees) I can have problems that my 35mm does not have. If I manually set the camera to what the AE prism states, or use the AE lock function (or even an hand-held meter), I'm fine. If I leave it on automatic I sometimes have problems. In Theory I think I know the problem, in Practice I need help/advice.

Although I don't consider the camera heavy, when hand-held the weight does seem to make a difference when trying to be still. I think this may be part of my problem.
I have, though, managed to squeeze off some 1/4-second exposures in a forest that are acceptable to me in a 4x6 print.

Disclaimer: I know what is acceptable to me may not be, and is likely not, acceptable to the more experienced and advanced photographers on APUG. So think of it in relativistic terms; improvement rather than perfection.