This was a fun romp through FreeCAD. I threw together a version 1 to test making watertight structures (and as an intro to FreeCAD). The trick, it seems, is to print slowly and with about 25% extra "width" in the slicer settings for the nozzle. That is, 0.5mm instead for an 0.4mm nozzle or 0.75mm for an 0.6mm nozzle. If it's making blobs of extra plastic, try dialing back the extra width. I printed my boxes in a combination of PLA and PET-G. The latter is a bit tricky because the layers sometimes don't stick together perfectly, causing leaks, but going slowly and turning the fan off helped a lot.