Here are the steps we used in Pender County Schools to create and manage our Minecraft accounts:

1.  To manage the accounts we created a primary account for the school district then, using it, purchased gift codes (20 in all for our program).  This required two separate purchases since you seem to be limited to purchasing a maximum of 10 at a time.

2.  Upon completing your purchase, you'll receive an email on the primary account with a list of your gift-able codes.  You'll also see all of your codes on the Profile page of the account gifting the codes.

3.  Create the student accounts on Minecraft.net.  We used a standard naming system such as builder_1, builder_2, etc...  Boring, yes, but since we were maintaining the accounts and are unaware whether a male or female student would be using them, we opted to be more generic.  We set them up using generic email accounts we were already using for other game-based programs through our district's Google Apps account.  If this is not an option for you, consider creating GMail accounts for this purpose.

4.  Once the account is created at Minecraft.net, click the Redeem Code link and enter code you've assigned to that account.

5.  It is highly recommended that you create a spreadsheet or Google document to manage this information!

6.  Once the accounts are created and the codes redeemed, distribute them to students.

Update

Created Avatars for the students at both of the schools (male and female versions)...

The male avatar is derived from the base model ("Steve") included in the game, and the female comes from the Jazzy avatar found on Minecraft-skins.net.