Crap. So far I have 2 sections. One for spawning resources which essentially I made collision boxes, and if they didnt overlap any other collision boxes then I spawn the nodes within the area. The same thing for the trees.
The difference for the water is I wanted to eventually replace the edges of a body of water with different sprites to make it look like the edge of a lake, I thought that using an array would be the best use. I still think it is so I may try to use a combination of what you taught me and my previous butchered collision boxes and go from there for now.
Ultimately I may just end up trying to figure out that noise plugin to generate the map more cleanly, or (sigh) re-do all of my coding to store everything into an array first, then generate everything afterwards instead of doing it in multiple steps.
I appreciate all of the help. Hopefully I can pick on your brain in the future