Well, I am not a specialist or maniac of Onsen, but I also noticed there are several different types of hot waters within the small Kusatsu area, all of which naturally should come from similar source (probably Shirane volcano?). Some are while opaque, some are transparent and has some black particle mixed in the water, etc. I understand that they are relatively strong in mineral(sulfur, i assume?), and if you taste it, you will notice some strong saltiness or sulfur taste in the water. I am not sure why the difference in the color, etc (but the variation is good, right?). Those are known to be effective for curing diseases from ancient times, and it sure has the feel of "healing", but I guess the contact is all through the skin, so nothing strong or serious (if you are concerned about the negative effect). Drinking them is no problem (less than bathing in it ), just salty water. People has been actually drinking that for cure of diseases for centuries. There's the drinking stand, or foot-spa place near Ubatake.
One thing is that the water is really hot there (actually, hot water is running down the gutter or the neighbor river), so that would be the major cause if any effect should come out. I once stayed there for a week dipping myself in Onsen several times each day ( sorry, that's what we Japanese do), and eventually, my skin got really dry and became irritated. My skin obviously got deprived of the skin oil, together with too much continuous stimulation by the salty hot water. That was obviously too much. But one or two days, I guess no problem, if you can get into the hot water (sometimes it is too hot you can't get in...).
What I really like there, is that the hot spring is really abundant, so no heat added or nor the water recycled (it just flows over).
I guess modern types of visiting Onsen has a nice locker system. Anyway, you can just leave the major property at your inn (hopefully there's a safe box there) and grab some coins and towel and go wander around. This is the image of the Onsen-hopping
http://www.kinosaki3928.com/kinosaki/images/sotoyu_title.jpg (in the bag, there are towels and purse and underwears, etc. i guess),
If you want any support there, I guess (if your inn has trouble in the language) you go to the center of the village (village office) where I believe there is a tourist guide who can communicate in your language ( I strongly hope so).