Welcome, Keith.
Don't get caught up in the need for notching your mortar on the substrate and miss the point of doing that. It's just one commonly used method of achieving the required mortar coverage on the back of your tiles and the substrate.
What you really want is to have 100 percent mortar coverage. You won't get that very often. What you must have is at least 80 percent coverage with good coverage on all edges and corners. How you achieve that is entirely optional.
If you mark your layout and make all your cuts first, you can probably lay them along with your field tiles and never miss a beat.
If you wanna set all your field tiles and cut later, you can just clean those areas of excess mortar while filling the waffles after as you pass by setting the field.
If you wanna cut and set the cuts as you go, you can do some combination of the above as John points out. A margin trowel will be your good friend in any event.
Or you can fill all the waffles first and do one of the above the next day. Some folks like to do that to make marking their layout lines easier. Then it'll also be easier to set those cuts by whatever means you've selected.
Lots of ways to skin that cat. You may not even need a notched trowel at all to set those cuts. You can key in mortar to the substrate and backbutter your cuts and set them so long as you get the needed coverage and can get the height right.
Get the coverage any way that's convenient for you, don't worry about how you do it.
My opinion; worth price charged.
