When you upload employer contributions with the census you need to set the appropriate override in the Allocation parameters. The override you set needs to match the employer contribution type you're uploading and the contributions need to be in the correct column on the census.
Note, the override has to be set before the Scrub/Eligibility task is run.
There is a very rarely used override to note, Use alternative Employee Deferral amount in match formula (requires entry of matched deferrals in a different census field). When this override is turned on you must enter the deferral amount the match is being calculated off of. This is often seen when the eligibility for deferrals and match differ. So you may have participants deferring for the whole year, but only receiving match for the deferrals made in the second half of the year. To enter the deferral amounts you would use the ftw Contribution Upload grid on the Other Import/Export/Report page.