How do I set up a 5% pension deduction.... not using the first earnings field only??

I have status and non status employees so I need to have two sets of earnings codes.  if I select 5% of gross it only looks at the first earnings box... so I can not make it work for both types of earnings.  How can I get the correct deduction to calculate using different earning boxes for each one?

For example I need to set up something like this.

Native exempt income:    1000

Pension deduction:  50

Fully taxable income     1000

Pension Deduction      50

The incomes must be tracked separately as they go in different  T4 boxes.  However, while saying the % deduction is on gross.. it only used the one single box to apply the 5% and does not allow you to select the box you need to work with..  Since there is a need to calculate it two different ways you can not do both that I see.

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