Migrating from a Windows NT domain structure to an Active Directory implementation can initially be an anxiety-ridden experience. You're basically replacing the core of your Windows network in one fell swoop.
To help ensure your upgrade doesn't go awry, follow these implementation tips:
Before upgrading the PDC, synchronize the BDCs with the PDC. Then, take one of the BDCs off the network, and store it for a few days after the upgrade. If your upgrade goes poorly, you can restore your network by shutting down the network-connected BDC and the PDC and promoting the stored BDC to the NT PDC.
You don't necessarily need to follow all of Microsoft's best practices for designing Active Directory. However, make sure you understand why it recommends certain practices before discounting them.
For example, in multidomain, single-forest environments, Microsoft recommends an empty root with the domains installed as child domains beneath the empty root. This is useful if you have a lot of departments because it makes it easy to move these domains. But if yours is a small organization, you might not need to follow this particular design recommendation.
You can install Active Directory using other DNS servers, but it's much easier to install and troubleshoot when you use the servers for which Microsoft created Active Directory. In addition, you're less likely to run into problems later.