Run down for this process:
To get the rough soul gems needed to upgrade runic tools to be able to harvest souls from r6 nodes / mobs, you need to mine non slate ore (maybe you can get it from slate) then craft either a knife or a hammer with the soul gem to get the tool you need.
To get the soul just keep farming till u get one. Then for explorations you will need 2 blood of any rarity (but the 2 must share a rarity) and some other easier materials and crafted at a rune crafting station.
Finally to hit mother lodes, (stone for minerals you will want to make p stones to give good stat upgrades to the vessel) (ore is gems for necklaces, rings and runic weapons) you will want the player with the passive training to have a powerful tool while the partner(s) will have basic tools with foreman (foreman debuff will stack so 2 people with foreman is good)then have them activate the take it down ability whenever its off cool down and just keep going through the mother lodes. The reason to have the person with the best training to have the best tool is because whoever deals the most damage in the first 1/3(need a double check on that) will have the nodes drop table snap on to their training. So after the first third or so everyone can then use their best tools to help speed up the process. Typically you will want a potion as well for gem and minerals as they will greatly help your chances of drops (you will need bones for these potions)
General tips: ravines will have lots of one type of node (stone or ore) but lots of mobs, keeps will have both types but more spread out and little to no mobs. For the foreman people a good idea is to equip villien exploration disc (don't forget to equip the passive too) as it will reduce the amount of basic tools you need to craft. (That soul also drops from quarrying)
Vessel wise: As I understand it, p stones (philosopher's stones) aren't required for vessels but they make vessels a lot better. Also to make the good p stones you will need an emerald tablet, otherwise you can only make p stones with 2 philosopher's solutions, with the tablet you make it with 4 solutions. Which is about a jump from +20 to +40 of a stat. To get the tablet farm boss tier(captain, chief, king) war tribes of r6 and above that are the fae looking ones or the satyr tribe.