There is not a way to change the order of designations from alphabetical.  However, if you utilize designation types, you can group the designations by type, then choose the order of the type you want to show in the dropdown.  To create designation types:
  1. Go to Fundraising>Donation Management
  2. Click the Designated Giving Tab
  3. Click Manage Designation Types
  4. Click Create Designation Types
Once you are done creating your types, you can then change the order they show by changing the order number on the left hand side.

To change the designation type for a specific designation:
  1. Go to Fundraising>Donation Management
  2. Click the Designated Giving Tab
  3. Under Actions, click Edit for the designation you wish to change
  4. When on 1.Identify Designee, select the Designation type in the dropdown on step 3.