Canada payroll tax Company tax id

Hello,

I couldn't find on the community exactly what my issue is.

In the Corporate tax IDs (P059081A) we have two CFEDU0's setup , with separate Tax IDs, xxxRP0001, xxxRP003, one of those is obsolete (has been for years).

We can't figure out how the U01 or U02 gets attached to a person.

When I look at the tax overrides for the employees (P770105) everyone seems to have the U01 on the E1 rate code field (which is ours RP0003) which is correct.

But when we run tax history reports, or the T4s, we have a handful of people with the RP0001 company tax ID which is incorrect.  We have had our IT group going into the T4 file before we print and export to change all the tax ids to 0003.  Obviously this is not the optimal way to deal with it.