I use Vendor Invoices/Payments to keep track of expenses for a specific job. I end up creating one vendor invoice for the job and add line items with categories. When I apply payments, it will automatically prompt me to match up with the associated credit card charge.
Here is the strange part - when I run an itemized expense report, the totals look accurate for the category, but I can't for the life of me figure out the breakdown for each item.
Example - Here is a vendor invoice I created for a recent trip:

Note that I had two line items (both under a travel subcategory). I then applied two separate payments of $163.24 and $191.96 to match up with a credit card statement.
Now I run an itemized category report and get this:
How/why did quicken break out those payments this way? I had another instance of a $6.99 charge being broken down into 4 arbitrary numbers. The total for the category seems to match up, but the breakdown makes no sense whatsoever. This gets progressively worse if I have more lineitems on that invoice as none of them match up to the actual figures.
I did a manual calculation of the amount spent and it matches the category but is off but a few cents. The only way this seems to work ok is if there is a single invoice and single line item for each charge (which is wildly inefficient).