Until such time as I can feel comfortable enough with the Scan Tailor code to make meaningful changes to it, I'm working with the same version as everyone else -- I've compiled it, but haven't modified it.
I thought I'd just toss out a couple of tips I've come up with.
When I'm going through page-by-page on the "select content" step, to make sure the page numbers have been selected and the gutters in the middle of the page have not, I prefer to have the mouse in one hand (to move the edges of the selection) and the keyboard in the other (to "page down" from one page to the next). For some reason, the "thumbnail" view on the right doesn't scroll by default when I'm using the keyboard, but I've found that if I go back to a previous step and say, deskew a page, then the scrolling will work thereafter for the "page down" key.
Often, I'll have a table or an illustration in the book that was printed sideways on its own page, and I'd prefer to view it on my monitor without tilting my head or flipping the monitor. However, if I just rotate it back to reading orientation, it's now wider than it is tall, while the other pages are taller than they are wide. In this case, I keep the same margins on the "page formatting" step, but uncheck the "align with other pages" box. That keeps this "wide page" from being considered when ScanTailor decides how wide to make the other pages, and I get a table in my ebook that's oriented for easy reading.
Usually, flipping a table page back confuses ST a little bit -- it wants to treat the wide page as two pages side by side, and will actually change the single thumbnail into two. If this happens, just go back to the "split pages" step and manually specify that it's a single page, and ST will probably be able to handle the content selection as it should.
Here's the process I've settled on for the "output" step. For most of the pages, the default black and white works fine, once I uncheck the "Despeckle" box. Covers and end papers of the book jackets I usually want in color. I'll start at the front of the book, and do the first one or two color pages, and the first black and white page. Then I'll let it run on auto to output the rest of the pages in black and white without despeckling.
Once that's done, I'll scroll through the thumbnails manually, using the scroll wheel on my mouse, looking for pages with illustrations. If the illustration is a line drawing, no action is required. If it's a photo or something else with shades of gray, I'll check the "mixed" mode for output and let ST grind through and output the page again. Usually, it finds the pictures automatically, and I can go on to the next. If it misses a picture, or part of one, I click the "Picture Zones" tab in the middle pane and draw around the parts it missed myself. I can zoom into the page using the scroll wheel on my mouse, and once I've zoomed in I can push the page around by clicking and holding the left mouse button. Clicking and releasing drops another "point" in my picture outline. The outline is completed by bringing the mouse close to the first point (the new point will "glow") and clicking to close the outline. Once the outline is complete, the points can be moved around, and new points can be inserted. The outline can be deleted by right clicking and deleting from the context menu. Once all the pictures are identified, clicking in the "output" tab does what it says it will do.
When I get to the end, I do the last page or two in color (end flap and cover), and I'm done.
Finally, I've gotten in the habit of saving my work. I've only crashed ST once, but I hate having to do things twice. I save the ScanTailor Project in the same directory as the input JPEGs, but I guess you can put them anywhere. I let ST rotate my images now, then go straight to an auto "select content" step. As soon as that's run, I save the project before I do any tweaking, and save periodically as I'm making subsequent changes. It's also informative to look at the XML file ST generates for additional insight into how it does things internally.