Settings Bundle
Settings work a little differently for jailbreak apps. You need to do something similar to the normal Settings.bundle, but there are differences.
See here for some information on that.
And here
And here
You should make your app depend on the preferenceloader
package, which helps jailbreak apps manage Settings. So, you'll have something like this in your DEBIAN/control file:
package: com.mycompany.MyApp
Name: MyApp
Version: 2.2-2
Architecture: iphoneos-arm
Depends: preferenceloader
Description: Do something for jailbreak iPhones
...
Keychain
In order to make the keychain work for my app, I needed to add entitlements to my binary. The way I found out which entitlements were needed was to first build the app in the normal way (not a jailbreak app, just a normal 3rd-party app store app using Xcode). Then, I inspected the entitlements in the binary built by Xcode:
ldid -e MyApp.app/MyApp
And then spliced those entitlements into a new entitlements.xml file. See here for an example of applying entitlements. I believe the entitlements for your app should look something like this:
<key>application-identifier</key>
<string>L44W4W8ABC.com.mycompany.MyApp</string>
<key>aps-environment</key>
<string>development</string>
<key>com.apple.developer.team-identifier</key>
<string>L44W4W8ABC</string>
It's possible that this method of adding entitlements isn't necessary. See comments below your question for other options. However, I was adding other entitlements for other reasons, and could not do that through Xcode.