In the future, please limit your posts to a single topic. You have 3 unrelated questions here, which will reduce your chances of obtaining answers because people won’t read posts they have no knowledge of.
First, what do you mean by linking a customer invoice (I assume you mean a sales invoice) with its related supplier invoice? These are distinct transactions in Manager (or any accounting system). Are you passing through a subcontractor invoice? Is there a billable expense? What are you trying to accomplish?
There is currently no report of profitability by job or client. To determine this requires extensive work to allocate operating costs across all customers. Job costing capability is third on the Roadmap.
Tracking codes were really meant for divisions of a company, not a constantly growing list of jobs.