The third photo is the bottom, right? It sounds like you’ve made the correct conclusion, that you need to calibrate the nozzle-bed distance better. Especially the dark filament looks like it was printed while the nozzle was too far from the bed. However I don’t know how you adjust this distance on your printer. On a normal printer with a single nozzle and no probe you would do this by levelling the bed at a different height. On a printer with probe you adjust the “probe z offset” setting in firmware. But since you have dual nozzles there’s probably some kind of calibration/levelling procedure specific to your printer that you need to follow. The transparent filament looks like it was printed at a better distance.
I would suggest that you try to improve the first layer before tackling the issues higher up.