Before you set up Enterprise Architect for use with MSDE, we recommend you run the project integrity check tool (select the Tools | Data Management | Project Integrity Check menu option) on the base project to upsize to MSDE. This  ensures the data is 'clean' before uploading.

Note: You cannot move a model from a source .EAP file of a version earlier than 3.5.0.

Warning: Before proceeding, ensure MDAC 2.6 or 2.7 is installed on your system.

Upsizing Your Database

Follow the steps in Upsizing to SQL Server to upsize your model to MSDE.