Buying an intangile asset. $xxmm up front (capitalized) and $2k per quarter until a certain milestone is reached. The length to the milestone is estimable. How do I account for the quarterly payment

Accounting systems reflect actual costs. On this basis the capitalised up-front payment and the quarterly maintenance payments are accounted for the cost you incur or paid. You may use a PV approach when preparaing a report to management to reflect the RoI at current values.
Regards