The only way to make your invoice look right for reimbursable expenses (and keep more than one expense in separate lines without giving away your markup), that I can tell, is to set the markup % at 0% and then add your markup to each expense manually. 

This is especially important for sub-contract labor that we use, for example, having an engine rebuilt at a machine shop.  I don't want to create an item for this because I will have to create two new items each time I hire another shop to rebuild an engine, which is annoying.  I also must have multiple line items because one line item will reflect non-taxable sublet service, and the 2nd line will reflect taxable parts that the sublet shop purchased on our behalf.  

Marking them up for me is pretty easy because I use a parts matrix I made in a spreadsheet that marks up lower-priced parts more than higher-priced parts.  You would think that with all of the "advanced pricing" QuickBooks has, they would be able to include something as simple as a matrix for calculating markup, but that disappointment doesn't belong here with this disappointment.  They start to get confusing. So many things could work right; it's like swinging a hammer at a nail all day and never hitting it...