Other questions

@Melyssa1  RE: We want to be able to have a column on our estimates and invoices where we can change the markup as we go. 

Unfortunately there's no way to create a column that impacts the invoice calculation. The custom field @Bryan_M  recommended will function like a memo/text and won't have any actual impact on the Amount.

Some versions of QuickBooks include a feature called Price Levels which may help. Check in your preferences to see if you have this feature. Start at Edit | Preferences | Sales & Customers | Company Preferences and see if you have a section there for Custom Pricing: