I am using inkscape to make township and range grids of state counties. I create large grids, and when I need only part of the grid, I create a new layer and put a rectangle around the area I need, export it as a bitmap, open a new file, then import the bitmap. After that, I need to shrink the rectangle down, and when this happens, sometimes some of the lines in the grid disappear or look gray or look thicker than the rest of the lines. How do I keep all the lines looking even? This actually happens in my big grid as well- I created a six box by six box grid, grouped all the lines, and then I copy it and paste it every time I need to add on a township- and even though it's supposed to be a copy, sometimes the lines appear to have uneven thicknesses and don't match up to the original grid line that I created.

Is there a better way to be doing this? I have bought a book about inkscape and look at forums but I can't find an answer. Also, I have zero idea how to write code- total novice here.

Welcome aboard!

There is a tool option in the select tool's controls, to scale strokes proportionally with objects, that may cause that.
Leaving it unset, the same stroke width will remain.

Also, by double lines running atop one another, they can appear thicker by the rendering, that you can only avoid by not drawing lines in the same position more than once.

There is an extension for creating cartesian grids built in, and there is an improved version of it, put together by Ragnar you may check:
http://www.inkscapeforum.com/viewtopic.php?f=22&t=13891

Good luck!