I've been tweaking those numbers a lot, and it's a nightmare to figure out properly. The system group in StarSystemsDefs.xml decides how many of which planets spawn, but it's random how many of each system you get, so you will get wildly different numbers even without touching the resource settings. The main issue is you want *some* Thulium and Prometheon, but not too much of it, and it's very easy to get way too much.
Then, you have map sizes and their base number and you may want completely different values making finding a 'right' setting impossible. If you just want more of both I suggest going to the abovementioned xml file, and just up the number of planets in 'asteroid' and 'outerzone' lanes for more Prometheon, and 'deadzone' for thulium. (SystemGroup at the bottom of the file) If that does not do the trick, edit MapSizeDefs.xml and up the base number of the map size you are playing. (this will give you tons more of the other resources as well though)
<MinablePlanetChance>1.5</MinablePlanetChance>
I haven't touched this one though, you might be able to fix it purely by tweaking that number and the planet spawn rate a bit. I've mostly tried to get the number of habitable planets right for my mapgenmod, Prometheon and Thulium generation has been a secondary thing to test.