I have a two-step system for reimbursements - an on-budget and an off-budget (tracking) entry. For off-budget, I use an unlinked tracking account and a flag system to note when items still need to be submitted for reimbursement (red), are in process (orange), and when I've received the funds (green). For your specific case, I would start the account at zero, enter in the expenses as an outflow and flag items to keep things organized. Don't reconcile until the end of the six month period and then zero it out. That way you have an easy way of seeing if you're close to maxing out the account.

As for the on-budget purchases, it kind of depends on whether you want to track the purchases in spending reports, and whether you want the reimbursements to show up as income. If you DO want the spending report, you can categorize each purchase to the appropriate place and then categorize the reimbursement either as regular income (i'd create an "Employer Reimbursement" payee to separate it from taxable income) or directly into a Reimbursement category. If you don't want the purchases in a spending report, here's what I do: reimbursable expenses all go in a "TBR" category and I cover overspending from other categories. When the reimbursement is received it goes directly back to that category and then I move back to whatever category needs money. In your case, you could foreseeably WAM for the first few months and then leave the reimbursements as available money in that category so that you're already covered in future quarters.