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Hi wizardmatt. Let me try and answer some of the questions.
How the TOC is setup is largely up to you. Most people have the master project with no topics in it. in this case the master TOC just needs to have the slave projects added to it which displays the slave TOCs in the order in which they are added. If the master project does have topics this is OK and you just add the slaves in the master TOC where you want them to appear.
The other questions you ask are a little more difficult to answer without knowing what format of help you are providing and a little more detail. In the scenario you refer to are you using redirection topics to display the content of a single topic (i.e. there are multiple references in various slave projects that really just display a single topic content)? If this is the case you only need to change the topic with the content.
Regarding the search function, it works across all of the slave projects as well as the master. I know of no way to limit the search to specific slaves other than excluding them from the compile (e.g. using conditional build tags). If you are using webhelp I know some users use a third party search utility which you may be able to use to limit the search to specific projects. There is also a way of "hiding" individual topics from the search but you'd have to do this on all the topics in the slave project which may be long winded for what you want. If you want this, you can find out how to do this in ACE Rick Stone's Tips n Tricks file.
Come back if you have any further questions
Doh! Just noticed from the post title that you are publishing webhelp.
Thank you for the information. You gave me all the information I needed to know. :)