You control that in the SSL layout when you create the chm.
There are two possible solutions for your work flow.
When FrameMaker content is imported in RoboHelp, RoboHelp imports all the Conditional tags and allows them to be turned On/Off independently. As suggested by Jeff they can be managed in Single Source Layout properties dialog. For HTML Help, you can click the "Define" button for Conditional Build Expression.
However, if you do not wish to manage the Conditional tags independently in RoboHelp, you can import FrameMaker content into RoboHelp with required conditions tuned On/Off as specified in FrameMaker. This can be done by turning "Apply FrameMaker Conditional Text Build Expression" setting on. Here is how this can be done.
1. Go to File->Project Settings dialog
2. Go to Import tab
3. Click Edit button for FrameMaker document conversion settings dialog to open Conversion Settings dialog
4. Select "Other Settings" on the left.
5. Select the check box for "Apply FrameMaker Conditional Text Build Expression"
6. Click OK on both the dialogs.
7. Update/Import FrameMaker content.
I hope this resolves the issue.