Manual entry — the project manager judges it. Simple, subjective, appropriate for knowledge work. Cost-based — percent complete derived from cost incurred against budget. Objective, and misleading — because spending is not progress. Effort-based — derived from hours against planned hours. Better for labour-intensive work. Deliverable or milestone-based — progress recognized when something is delivered. Most objective; requires well-defined deliverables.
The cost-based trap. It is the easiest to automate and the least meaningful. A task eighty per cent spent may be thirty per cent done — and the one method that reports purely on spend is structurally incapable of noticing.
Deliverable-based where deliverables exist. Effort-based for labour tasks. Manual only where nothing better applies. Avoid cost-based unless the client insists and understands what it means.
Mixed methods. Different task types can use different methods on the same project. That is usually right, and the lab requires two.
CONFIGURATION CANNOT FIX A CULTURE WHERE NOBODY REPORTS BAD NEWS. Whatever method you configure, the number is only as good as the person entering it. You can make the honest answer easier to give. You cannot make somebody give it.