It is basically impractical to amend a Form 1023 application for federal charitable tax-exempt status if the IRS does not ask specific questions on its initial review.  Having reported that you owe your officers back compensation, you should just go ahead and pay them when you have the funds.   There is no process for getting IRS approval and no need to seek it.  Assuming that the compensation is reasonable, the IRS will have nothing to complain about.  You are doing what you said you would do.

Even if you hadn’t reported the situation on your Form 1023, the IRS is accustomed to having organizations deviate from the statements made in their applications for exemption. If the IRS subsequently audits the organization, it tends to be primarily concerned that the actual activities are charitable and comply with the relevant federal rules.

Your having reported the obligation on the 1023 will help reduce the likelihood that the compensation will be challenged as excessive. If you had held the payment for a few years and made it all in one year so that it appeared to be two or three times what you actually paid for work done in the year you reported it, you might have raised an excess benefit tax question with compensation two or three times normal and no longer “reasonable.”  You might also have raised state fiduciary duty questions about paying people for past services when you had no obligation to do so and were therefore “wasting” charitable assets.

It is always better to report your finances accurately.  If you run your organization correctly and transparently, you reduce the possibility that the regulators, donors or the media will have things to complain about.