BKChem and Inkscape are a great pair, BKChem is good at Chemistry and Inkscape is good at everything else. There are, however, some issues which make life difficult, i will collect them here:
1. BKChem and Inkscape do not use the same fonts by default, to solve this look here.
2. When opening a bkchem-svg with inkscape, inkscape messes up the font size. Import instead.