There are various documentation references to saving your SEB configuration by clicking on a button in the Preferences panel, to "Write into App Bundle," but I have no such button.
Here's a screen shot of my Preference panel:
Seems you're referring to the documentation for SEB 1.5.2, that feature was available there (only in the non App Store version).
You're apparently using SEB 2.x, documentation for this version is at:
To understand how SEB 2.x is intended to be deployed, configured and used in exams I would recommend to have a look at the presentation at http://www.safeexambrowser.org/presentations/HowTo_SEB2.0.pdf.
The feature "Write into App Bundle" was removed from SEB 2.0 because it's generally not usual to change an application's bundle and also because Apple doesn't allow it for Mac App Store apps. SEB 2.0 is using the .seb setting files instead which allow to initially configure a SEB exam client or to change its configuration on the fly for each started exam.
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