I left my default GPU setting at 64. Will this affect my installed packages in a negative way? I have a raspberry pi 3 and I am getting the hang of things so if there is a better setting I would like to know what it is and why? Thank you in advance!
The setting doesn't affect "installed packages" specifically, but affects the amount of memory you have available for graphics operations and how much system RAM you're left with.
You need at least 16 MB of graphics memory for the system to run at all. That's also enough for a 1920x1080 16-bit color display, or even 32-bit color (though graphics memory might get a bit tight there). Graphics operations that use the GPU, such as video decoding may want more GPU memory. The biggest use of graphics memory would typically be games, especially 3D games with a lot of textures to load in to memory.
More system RAM is always a good thing; even if you have plenty to run your programs, "unused" RAM will be used to cache disk (SD card) data, giving you faster access to files in many cases. There are a variety of different tools available to help monitor how much memory is currently in use, but I find
htop (in the Raspbian package of the same name) to be the most convenient.
It's perfectly safe to play around with your memory split and see what the effects are. The answers to What is the optimum split of main versus GPU memory? will be helpful to you here.