I work primarily on battlemaps, so my comments below reflect that.
My process involves several programs: Inkscape for making masks for key areas/walls, Paint.net for grids and DPI adjustments, and Photoshop for the heavy lifting. I use grids throughout. The procedure goes roughly like this:
1) Decide the dimensions of the map in inches, and the desired output DPI. I generally do 100 DPI. For online use, that tends to generate tolerably decent file sizes (especially if you tweak the JPG compression ratio rather than just accepting the default). For print, 100 DPI looks okay. 300 DPI would be better, but my computer tends to struggle with larger maps at higher resolutions.
2) Open Inkscape. In the document properties, I set the dimensions to the desired size (say, 2000x2000 px for a 20x20 inch map at 100 DPI). Also in the document properties, I create two grids: one grid repeats every 100 px on both axes. The other repeats every 10 px on both axes. For the smaller grid I check the box for showing dots rather than lines. The larger grid defines the basic squares of the map, the smaller grid makes it easy to create regularly-sized doors and things, because I have 10 subdivisions of each square.
3) I draw in a mask for the thing I want in black, then I export it as a PNG. For example, here's a platform made up of large, rough-hewn stones that I made for my Erobelis Entrance map:
Inkscape has a super-weird concept of DPI that doesn't conform with anyone else's. In order to export at 100% of the designed size, you have to set the DPI at 90, and every other graphics editor is going to see it as 89.99 DPI, which is bizarre.
4) Here is where Paint.net comes in. I open up the exported image in Paint.net, use the Image Size tool to adjust the DPI up to 100. Then I add pure white under the black outline of my mask, then invert the colors (so my desired object is white), flatten the layers, and save. This could definitely be done in Photoshop, but I figured out how to do it in Paint.net long before I learned Photoshop, and have just continued doing it there out of habit. The previous image was adjusted in this way, compared to the default Inkscape output.
5) At this point, since I have Paint.net open, I use the Grid Maker plugin to make a grid image in the same size. Typically I use white lines on a transparent background, with a width of 3 px or so. Like so:
6) In Photoshop, I set up my grid preferences to use 100 px steps, with 10 subdivisions, exactly as in Inkscape. And at this point I can take the mask and grid that I generated earlier and put them all together. Here's a PSD at this point, cropped to save on file size:
And a JPG for those that lack Photoshop:
It's pretty basic -- a layer of dirt texture, a layer of rock texture with the mask and a bevel filter, and the grid as a layer on top (overlay mode, 60% transparency, gaussian blur 2px for blending). It's a bit hard to see the white lines on the white-ish stone in this example. If I were developing it further, I'd probably swap in a darker stone texture, or else lighten the dirt and then use black lines (with multiply) instead of white lines (with overlay).
So to sum up, I use grids throughout. The key is using consistent dimensions and DPI settings between applications, and then everything lines up. And that is probably way, way more answer than the question needed!
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