Your post was slightly confusing, so let me see if I understand. You want to put a custom 3do into a level you are making?
1. In the project directory for your level make a subdirectory called 3do (if it doesn't already exist). Put the new 3do(s) in there.
2. If the 3do uses new mats, make a mat subdirectory and put the new mats there.
3. You have to create a template. I suggest you read the templates tutorials here at Massassi. Some custom 3dos (a lot of the new enemies for example) have premade templates you can just copy and paste into your master.tpl file.
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