They will execute with normally on a Mac, the encoding is for when they are transferred to a mac.

You have to transfer them somehow, either on CD or across a network, when on a CD if you follow the tutorial in this forum's FAQ it explains how file is decoded as part of the creation process.
If you're transferring them via a network, it's normal to have a file zipped and have to unzip it the first time; decoding will happen at the same time as unzipping.