When you upload employer contributions you need to set the appropriate override on the Allocation Parameters screen. For regular match this is 'Match allocation manual override'; for Safe Harbor match it's 'Safe Harbor Match allocation manual override:'. The override you set needs to match the employer contribution type and the contributions need to be in the correct column on the census.
### Note that the override has to be set before the data scrub is run. ###
The first override option in the allocation parameters section is 'Override Employee Contributions to be matched (requires entry of matched contributions in census)'. This is used very rarely, when you are calculating match, and eligibility for deferrals and match is different. 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. If you use this override, you need to add the column: 'R:MatchedEmployeeContrib' to the census grid, and use it for deferrals being matched.