Ok so the charges on the staff are separate to the runes required for casting the spell. When you finish UP the staff has 120 charges. So every time you use the spell, it costs the runes to cast it and 1 charge from the staff. You don't charge the staff with the runes, but you still need runes to cast the spell if that makes sense.

you can then pay the guy in West Ardougne (200k i think) to upgrade it so that it can carry 2500 charges instead of the 120. This is absolutely essential really or you'll spend so much time recharging the staff it won't be worth using. The staff/spell were pretty much total trash until they added this update.

When you recharge the staff, you can either go back through the underground pass and use it on the altar or pay (again, i think its 200k) for the guy to recharge it for you. I would recommend completing also regicide, Roving Elves and starting Mournings End pt 1 which gives you the teleport crystal. This allows you to teleport to the other side of the underground pass and enter it from the elven side which is closer to the recharge altar/well than the ardougne side. 

Regicide is the biggest ball ache out of all those quests as you have to go through the underground pass twice; altought by this point you should be able to get through it pretty quickly. 

happy to help if you need any more info bro.