The way to tell which service needs to be done is by how many wrenches show in the display. One is for schedule A, one on top of another is for schedule B. A should be the first one.

On the transmission issue, the way I interpret the manual is that you change the fluid at 80,000 for the automatic and then never again. You should never have to change the fluid on the manual transmission. The manual doesn't even mention ever checking the fluid level, which seems a little scary.

If they are trying to charge $344 for the service, they are trying to screw you and charge for a bunch of unnecessary stuff. If you have them perform all the necessary checks, it shouldn't take over an extra hour on top of the oil change. That should be about ~$70 labor on top of the ~$80 for the oil change. Most everything on there is a visual check that most people should be able to do themselves.