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You need to use ODT to deploy a .NET stored procedure however if you need to deploy the same .NET stored procedure to multiple databases then you can manually copy your stored procedure DLL to $ORACLE_HOME\bin\clr (or whatever your deployment folder is) and execute the PL/SQL script generated by the ODT. (The PL/SQL script can be saved in a file just before deployment.)
As Skj said, you need ODT to at least generate the deploy script (you don't actually need to perform the deployment with ODT, just generate the script).
The last screen of the ODT .NET deployment wizard offers a chance to save the script to a file. You can save that script and then cancel the wizard, and from there on do everything manually, as skj mentions.
Post back here if you have further questions.