You can achieve this by configuring rules in PE51. Try the below(have assumed the wage type in question is /552, if not assign the rule to the appropriate wage type):
1) Tcode Pe51, selection the Rules radio button. Create two new rules with the following values under the respective column, leave all other columns blank:
Rule No. Table field Typ CO Value 1
78 1 XRT BETRG N LT '0
79 1 XRT BETRG N GT '0
The first rule checks if the wage type amount<0. This rule should be assigned to the wage type in the Deductions window & in the Deductions cumulation id,since the wage type should be shown under deductions only if the value <0.
The second rule checks if the wage type amount >0. This rule should be assigned to the wage type in the Earnings window & the Earning cumulation id since the wage type should be shown here only if the value >0.
2) Earnings window
Add the wage type(/552 or the appropriate wage type) in the Earnings window. Assign rule 79.
3) Deductions Window
Add the wage type (/552 or the appropriate wage type) in the Deductions window. Assign rule 78. Assign conversion 19 (no +/- sign).
4) Earnings cumulation id.
Add the wage type to the Earning cumulation id and assign rule 79.
5) Deductions cumulation id
Add the wage type in the Deductions cumulation id, assign rule 78, enter MS - so that the value is subtracted. (since the negative value should be subtracted).