I.e. a customer picks profile x & it requires us to retool a machine so I just want it charge once for the order when profile x is selected.
Since attributes and price adjustments always function per item, the only way to add a one-time upcharge for the tooling charge situation you're describing is to manually add the upcharge after the order is placed - that means if it's a $10 additional charge you'll want to convert it to an itemized order (button on the bottom of the side bar on the order) so that you can add $10 to "other cost." And to make sure someone knows to add that $10 charge you may want to use a trigger that fires when the certain profile is chosen to tell an employee that it needs to be done.
The other idea, which is more in line with how we think the best way to handle the cost, is to build it into your pricing (aka just increase your price a tiny bit) - say the bit is $100 and it can do 200 doors before you need to change it, that's only .50 per door.
And as for chrages that apply per 10 items, I also recommend doing that in your pricing formulas. You can use logic in your formula to say something like "if less than 10 doors, then add $20, otherwise add $0" by writing a formula like this and adding it to your other pricing sections:
(part.panel.qty < 10 ? 20 : 0) ---Note that I just made this variable up and you'd use the actual variable from your instance - the best way to get a quantity that tells you the number of doors ordered is by using the number of panels from your parts (let me know if you need more explanation here)