An Allocation record is exactly how that opportunity will be applied to a given Fund. Even if the opportunity is only going towards a single Fund, an Allocation record will be created. You can find the Allocation related list on an opportunity and it will show the exact Amount and Fund. The total of the Allocations should match the total of the Opportunity. If the opportunity is split between multiple Funds, there will be separate Allocation record for each split.

As long as a payment record is not marked as paid the allocations on the payment will stay in sync with the allocations on the opportunity. They will stay in sync with the percentage based on the payment amount and the Allocation percentage split from the Opportunity.