I'd put one skillpoint in encumbrance. It's worth it, even when you have the storage, I think.
As for scrolls: Once you have your enchanter (and alchemist), talk to them (I think you have to go into the actual "enchant" and "brew potion" menus!), all "new" ones get removed from your inventory, as your guys learn those formulae.
That means that after you did that (talking to alchemist/enchanter) you can get rid of all scrolls you still find in your inventory, as those are already known (and thus did not get removed) to them.