If your using the vbulletin enhanced integration those are options you do not use as header footer are for photopost non vb3 where we use our own header.
Now as far as getting into admin panel as long as the license number is correct in our config and you correct your cookies in vb
and photopost to be this you should not have to login twice.
cookie path /
cookie prefix bb
cookie domain .domain.com
As far as links to forum photopost etc you can edit your vbulletin navbar template and place links directly in there like so
Content visible to verified customers only.