IANAL: You probably should hire an accountant for your firm...since question answering is part of their job it probably will not cost you anything beyond the standard cost of preparing your taxes.
BTW, I would not be surprised if the way that you handled the initial purchase of the domain affected the resale. If you deducted the purchase price as an expense, you probably can't use the purchase price as the cost basis of the capital investment.
In other words, how to handle the eventual sale of assets is a question others should be asking their accountants.
(NOTE, the NIC fees are fees...not the purchase price)