Well the feature you are taking about (the red squares turning green when cleared) is an option that can be toggled on/off in the editor. It's called TRACE and it's in the C2ISTAR module.

What kind of problems are you having making your own mission? Just this?

You need to update your ALiVE. "TRACE" should be an option in that photo. It was added when ALiVE updated within the last day or so. If you see it in the CQB module, your ALiVE needs updating!

For a simple respawn system, assuming you're playing as BLUFOR, you need to have respawn markers on your map.

So place an empty marker and call it respawn_west

For multiple spawn locations you'll need to number them. So respawn_west1 respawn_west2 etc.

You'll also want to add your respawn of choice to description.ext. Here's a link that should help you. https://community.bistudio.com/wiki/Arma_3_Respawn

Well I actually go into the marker section, find the one called "empty," and place it where I want to respawn. When playing as BLUFOR I name it respawn_west. You need to rename it for it to work.

Then in your description.ext, type: respawn = 3;

For multiple respawn points you'll need multiple markers and some additional stuff in your description.ext that I'll need to get you when I'm around my computer. But what I described above should get a basic respawn working for you. Pretty sure I didn't miss anything.