I am having an issue where I need to be able to specify the password when I run my packages.

This article http://support.microsoft.com/kb/918760 says:

Method 3: Set the SSIS Package ProtectionLevel property to EncryptSensitiveWithPassword
Change the SSIS Package ProtectionLevel property to EncryptSensitiveWithPassword. This setting uses a password for encryption. You can then modify the SQL Server Agent job step command line to include this password.

That all sounds well and good. But where and how to you specify the password?

Here is an example of my current command line:

/FILE "C:\Program Files\Microsoft SQL Server\100\DTS\Packages
       \MainSSISPackage.dtsx"  /CONFIGFILE "C:\Program Files
       \Microsoft SQL Server\100\DTS\Packages\DataConfig.dtsConfig"
        /CHECKPOINTING OFF /REPORTING E