Benefits such as Pag-ibig, SSS, and Philhealth must be coded as a bill in Xero along with a zero tax-exempt tax rate (Tax Exempt (0%)., and they should not be pulled into JuanTax.
However, you can use the 1601-C report (Monthly Remittance Return of Income Taxes Withheld on Compensation) in the Standalone version to enter these kinds of transactions.
Visit this article for you to learn the steps in adding 1601-C reports in JuanTax.