I believe you could have kept the same SSP for your sites, so that may be extra baggage.
If I am keeping up, then you wanted to create a New Web Application (using the original SSP should be fine) called Intranet2. Then from there, create a new Site Collection, and choosing which template you want (Collaboration Portal for example from the Publishing template category). Then from there begin building your new site. The Publishing templates give the multiple top row. If you go to Site Actions, then Site Settings you can manage the top row.
You really only need, to my knowledge, the single SSP. Not one for each site. I have a few, about 5 or 6, separate sites running on the single SSP. One of which is public, the others are Intranet. The Alternate Access settings help with this, combined with the Host Header and DNS.
I'm sorry if I'm on the wrong track. I did not realize how tricky this would be, meaning posting, without actually seeing stuff.
JohnQTech