tabs - base layer
content
replays

divide your project into the three key blocks you need so they all hold a fairly even amount, leave the junk inputs you never touch during a broadcast unassigned and they will be in all (the grey tab)

inputs are in order and your commands are assigned to the input number ie on completion- cut to input 11adverts... if you move your input11adverts it will cut to whatever is in input11.
Seperate note, you can rename the inputs in the settings / general / click on the title, for more organisafiying.

not sure what you mean with the last question but remember when sorting the project to put things you don't want to clash on the sane overlays

and lastly set up two projects - clean and demo.. in the demo just go nuts don't worry about the mess and just see what everything does and almost try and break your set up (what I call clashes) as you slowly construct your filtered version in your clean set up.
The aim is to get rid of the 'hops' amount of buttons you have to press to execute the task right down to getting your equipment set up in the least amount of steps. Vmix is the best broadcasting software and with the triggers and automation if you spend the time you can do anything you want with it )