Duplicate Expense accounting

I have recently come to the understanding that when reimbursing employees through Payroll and having no expense payments going to vendors, except for Period End Accruals, journals need not be created from EX_ACCTG_LINE (meaning, Post Liabilities & Post Payments need not be run at all). Journals are created from HR_ACCTG_LINE, alone, when HCM completes their processing and this documents for the GL, all departments' expenses incurred for the period.

This would all be fine and good if we were not paying corporate card vendors out of AP, but we are. AP needs accounting entries to be made before generating payments, right? So we run Post Liabilities and debit expense/credit liability. AP offsets the liability for vendor payments when checks are generated but this leaves me with two issues: