Multivideo.info have some features not present in Multivideo Editor. You must edit the XML multivideo file directly. For that, you can do:
1.- In multivideo site: when editing a multivideo.info select "Advanced (XML file editor)".
2.- In your site: just create a multivideo xml file, and put the url on embed code. Maybe you must put a crossdomain.xml file in your site to make it works.

Pause

You can add pauses on your multivideo.info.

Just add in beginning of the xml file, after <linkbase> tag:
<pause>00:00:05:900</pause>

Where the 3 last digits are miliseconds

Begin video at

Just add in beginning of the xml file, after <linkbase> tag:
<v_sec>266</v_sec>

Begin target video at

Just add in action part:
<start_target>00:00:10:200</start_target>

Goto current video at

In link->action, the target video must be the same than current, in:
a) "action_type" value and "youtube_id" value (by now), and/or
b) "multivideo" value

And you set the time of the current video to go to:
<start_target>00:00:10:200</start_target>

Custon shapes

You can add custom linked shapes. Just create a flash movie with the same size that your video. Everything that is not empty on your swf file will be linked. For opace parts, you can set the transpatent percent on multivideo.

Just add in the xml file, on linked section:
<alpha trans="10"\>alpha_entel.swf</alpha>