I actually read through all posts to make sure I would be relevant. There was one post that might of been my solution, but it wasn't clear. The way I figured this out for me is that there are 99 user presets. To start, I decided to build my library at 50 and up. For gigs, I would use 1-49. If my library got bigger, I would either save some less-used patches on my computer, or start going down into my gig space. For a gig, I start at 1 and put any patches for that song in a row, usually one per song. If you stuck with one patch per song, you would just do one tap between each song. If you go back to a patch, just make a new copy in the next space so you don't have to go back. I put the patch number(s) on the play list, or sheet music to reduce confusion/panic in a gig.
For multiple patches, use the next 2-3 for that song and you only have to tap up or down once, or in extreme, cases twice during the song. It gets more complicated if you start playing out of order, but holding down the up/down button lets you scroll around quickly. If you do this often, then the computer interface is easier to make big jumps like that and may be worth having on stage. Even then you only do this between songs because your patches are still grouped together.
As far as bypassing, A patch with no effects is good and you can even put a copy of the same bypass in every song group if you do this often. The one adjustment I would use on that bypass patch would be the master volume since you have volume and eq settings in the other patches. This helps you keep a consistent volume throughout your patches. In fact that bypass patch could be used, when creating or bringing a new patch into your user library, as a volume standard to set the other patches by. If you are a purist, then I guess that is what money and physical switches are for.
I have spent a few days with the software. It really helps to understand and create patches down to the smallest detail. It would not be a good tool to change patches during a song unless you have long breaks.
Some interesting things I noticed is that using only the mark pre-amp with my MarkBass pretty much sounds the same as plugging directly into my amp. There is a big difference between using headphones and then using the same patches with my amp. The amp needs a lot more love put into the patch before it sounds good. I appreciated the comment about creating two libraries: Home/headset and Amp copies. I will start doing that.
As far as zoom/Boss/etc. and what sounds best, that is up to the individual, but with the method above and the abundant library space on the unit, I see the 1B as one with the most pros and ease of use, especially with a computer. Of course that last statement is specifically due to my wants and needs.