I have a 2 machine config: FMSA11 on one SL server & web publishing on another SL Web/domain server. Can you tell me which type of SuperContainer (SC) installation I should perform and on which server?

Goal: to best enable IWP for SC, allowing preview of pdfs in IWP, over an SSL connection.

Install Option 2: Installing SC with FileMaker Server Advanced (but on which server, the "worker" with web engine, or the "master"?)

Install Option 3: Installing SC with Tomcat (which is a manual installation for Snow Leopard Server). Will I lose webviewer interactivity by using this method?

If I have a CA installed on the web server, and SC is also installed there, are there other installation procedures to perform to get SC to work properly via a secure web connection? (ie: changing the root folder path, the ports, etc.)

You should use Option 2, this will let SuperContainer piggyback on the FileMaker/Web Server setup and your SSL settings will be automatically extended to SuperContainer.

but on which server, the "worker" with web engine, or the "master"? And... I'm assuming do a manual install since it's SL...

All of your FileMaker web traffic (including SuperContainer when deployed with FMS) is run through the machine running the web publishing engine. The purpose of the two-machine deployment is to run the web server on a different machine from your database server, and so the machine running your web publishing engine will be the one you need to configure your web settings on.