He turned out to be a bad apple that did good work but then grossly overcharged above the agreed upon amount.

If they're overcharging you however, then I'd suggest getting a new management company, as I don't believe that's an ethical way to do business.  

Study , study , study ... oh ya .. you better learn how to estimate a rehab project .. you need to know if a contractor is over charging you .. learn about contracts .. and learn about construction codes .. 

So with a fixed price I'm worried that I may be overcharged in some areas and not get discounted when I downgrade items (such as cabinets), or it was calculated into the fixed total and turned out to not be required. 

If you are attempting to make more than 6 to 10%, varies with the type of property, and you're doing nothing more than facilitating a transaction, you'll be in the liar and cheat category, regardless of how you try to justify what you're doing, because facilitating only carries so much as a value, anything above that is overcharging.......period!

I also was not willing to go the route of suing for about $2k worth of overcharges (amongst other general complaints), especially because we were getting ready to list the house and didn't want any liens or other legal things to wrap up.

When things go bad, they blame the property manager and lump all of us into the same pile of "do-nothing, over-charging thieves" instead of taking responsibility for their own choices.Choosing a property manager is a lot like choosing tenants.

I don't let my Property mang. take care of small issues because they over charge.

I know he is overcharging, he quoted firstly on 3 panels then he cut off 2 off them and combined everything to 1. 

This person may not be overcharging but may be doing the job right by using quality materials, quality tools, actually has the knowledge and the business license and insurance to back it up.