Why do I have two accounts with the same email address?
You most likely used the same email address to use products, such as AdWords, that were previously only available for Google Accounts while using the same email address to use products that were available through Google Apps. After this recent transition, Google Apps accounts are able to access the majority of Google products, including AdWords, just like a Google Account. As a result, you have a conflicting account.
A conflicting account is an account hosted on the Google Account infrastructure, created with the same email address as your Google Apps account. Having a conflicting account means that you have two accounts with the same email address, hosted on two different name storing databases.
When the Google Apps account transitions into the Google Account infrastructure, only one instance of the account name can appear in the Google Account name database. To resolve this conflict in account names, the data in the personal Google Account will need to be re-associated with a different account name. The next time you sign in to your conflicting account, you will be asked to change the name you use to sign in, in order to continue accessing the data in your conflicting account.
For instance, your Google Apps email address is firstname.lastname@example.org. A while back, you may have signed up for AdWords with this email address, which created a personal Google Account. Since we've moved your Google Apps account to the Google Account infrastructure, your the data in your personal Google Account will need to be re-associated with a new name because there can't be two email@example.com accounts with the same name. The first time you sign in to your conflicting account of firstname.lastname@example.org to access AdWords, you will be prompted to re-associate your data to a different account name. Once you do so, you'll need to use the new account name to sign in to AdWords and access your AdWords data.
After the transition, keep in mind that you won't be able to sign in to multiple Google Accounts at a time. If this is a problem for you, learn how to get around this issue.