For the Alchemist tree you must find other scrolls (Formula's) they are stronger. (Limited is lowest, Ultimate is highest)
And don't mistake with the Formula's for Enchanting ... possible you have much of these scrolls, but not all are for making potions

The stones you mentioned are
Charms you can put on weapons and equipment-items.
Each charm-stone you put on something you CAN'T do it away: it is fixed.
On the other hand, Enchantmentslots you can make back empty and put another in.
how or where do i use them???
Do you play on PC or Xbox?
On Xbox:
go to your Equipment and find an item that have a empty charm-slot. Than open the menu of that item (select it) and at the botom of the screen you see a yellow button that explains:
"Y = Charm" . Push Y on your gamepad and select a charm(stone) you want.
For the PC I don't know how it works.
Maybe reading your Manual can help?