It doesn't matter what kind of numbering system you use, just make sure it's in sequential order so you don't get confused.
Be transparent – Your client wants to know where their money is going, so don't hide or be too general with line items on your invoices, and be prepared to show receipts. Otherwise, they'll wonder if you're padding the bill. Be specific. For example, instead of listing "materials" as a single expense, list each one on its own line, such as: paint, nails, plywood, etc.