Logging does a good job of telling you where problems are, and I have never noticed an issue w/apps causing problems other than in the specific automations create in them. It is good to map out what you're going to automate and then choose the app appropriate to do the automation in. So install them, look at their capabilities/settings, and then you'll make better choices.
You should be able to create most of your automations using a few built-in apps:
- Motion and Mode Lighting app
- Notifications app
- Simple Automation Rules app
- If you are more techie/programmer, you may also like Rule Machine for more complex automations
There is a very very useful app called Hubitat Package Manager that allows you to easily install and update community developed apps and drivers from a central location...not every community app and driver are available in it, but most of them are. Having HPM is a must. It says "Beta" but it's very mature and very stable:
Just a few very useful apps you can get from HPM:
- Auto Lock (get the Auto Lock app version by Lewis Heidrick). Very cool app allows you to auto-lock doors and has a ton of customizations
- Auto_Off - There is also an "Auto off" (no underscore). Auto_Off is an enhanced version of the original "Auto Off" and has some additional features that make it nicer to use. Turn off any devices after a time period you set. Very useful.
- Advanced Button Controller - great app w/great options to set up and use your button devices.
- Event Engine: Automations app that provides more capabilities than Simple Automation Rules app, but is point-and-click and much simpler than Rule Machine.
Don't touch the Z-Wave Repair button unless you get written permission. 
Route changes only a problem if they become a real problem and you have mesh/performance issues. Go ahead and let your devices and mesh settle in.
Have fun setting your stuff up! 
