Just have the bot not pick them up. I collect enough wisdom/portal scrolls and then disable them in the item filter. Whetstones and scraps I have completely disabled, because it's a waste of time picking them up and having to deal with them when you organize your stash. By default, the bot will pick up and stash ALL currency. I'm not sure if there's a different way to do it, but what I do is disable the currency filter under "Pickup Filters", and then add my own custom one. You may already know how to do it, but I'll give you a detailed explanation in case you don't! Pretty simple. On the main bot screen, select "Tools" and then click "Item Filter Editor". Click the arrow next to "Pickup filters", and left click "Currency" to highlight it, right click, and then select "Disable Filter". Next, left click "Pickup Filters" to highlight it, right click it and then click "Add Filter". You should see a "New Filter" filter show up at the bottom. Left click it, and it'll open up options to the right. Click the "Names and Types" drop down, and paste this into the upper section.
Blessed Orb
Cartographer's Chisel
Chaos Orb
Chromatic Orb
Divine Orb
Eternal Orb
Exalted Orb
Gemcutter's Prism
Jeweller's Orb
Mirror of Kalandra
Orb of Alchemy
Orb of Alteration
Orb of Augmentation
Orb of Chance
Orb of Fusing
Orb of Regret
Orb of Scouring
Orb of Transmutation
Regal Orb
Vaal Orb
Click save at the bottom, and you're all set. Just close the screen. Make sure it saved by opening up the editor again, and opening the new filter. If anything is in there, you're good. You can remove/add whatever to that list any time. Wisdom Scroll, Portal Scroll, Blacksmith's Whetstone, etc. Keep in mind it's case sensitive, and make sure you spell them right.