If you check the wiki, it tells you how to do it. https://www.warzone.com/wiki/Map_Making
Set the document size: Go back to "Document Properties" and under "Custom Size" set the Width and Height to about 900. Ensure the units says px (for pixels). You can adjust the size for your own map's needs. (Note about map sizes: Most maps work best when they're less than 1000x1000. If army numbers appear too small when you test your map, that means your map is too big and had to be shrunken down, causing the army numbers to shrink. Thanks to the magic of SVG, you can reduce the size of your map without losing any detail. If you're making a super large map, note that the maximum map size is 3330x2400.)
So, yes, you should use pixels and only pixels.
If your map is to small, simply marking all your stuff in inkscape and resizing them should work? (then just uplod to WZ and adjust until you have a nice size). For reference, a bonus box's standard size is 16*16.