From what I understand, I should be able to add additional storage modules to cars, aside from just the slots assigned at the Car Lift. What I mean by this, is that I should be able to make them stack. 

What I'd really like to do is make a standard Storage Module, then use Quests to unlock a 2 module unit, and a 3 module unit. Essentially allowing a player to triple storage if they do the quests. 

Is this possible? 

It's already possible to stack additional storage containers on top of the car storage modules. Look at the default config in the documentation for an example.

However, while the plugin supports stacking RHIB storage and HAB stashes on top of car storage modules, it does not support stacking actual storage modules on top of storage modules. I briefly experimented with that recently, but there were some issues. Most notably, the plugin needs to be updated to support it, but there were also some visual issues like additional bumpers were showing on the extra modules, and I'm not sure if that will be fixable as it may be client side.

I appreciate your reply <3

In the future is there a way to add a permission based system to apply these changes? Example: normal players get normal vehicle storage, but VIP players get a RHIB box on top of theirs. 

Yes, that's already supported, according to vehicle ownership. The default config in the docs already does that.

Thank you!