This is how the JD Plus works (no need for JD Ultimate b/c we don't have many of the functions it supports. I just copied this from another thread the OP started awhile ago and I was trying to helps him out there.
If you set it to custom, the go into the settings tab on the right and then all the way at the bottom, there is two buttons to push, The first in Interactive which will pull up Juice Defender for up for any app that isn't already configured and the other is Configure Apps. This is the one that you can customize on an app-to-app basis where if you are no using an app and the screen is locked, it kills the radio/data traffic for that app.

Say you are listening to IHeartRadio, this you would want either Enable or Enable/off (which means the screen will be locked but the radio/data will be working). Now take the browser. It you are not using the browser, then you don't need it transmitting data right? So you would set that one to Enable (which means that it will only enable data traffic when that app is being used).

Juice Defender only works when the screen is locked, don't forget and all widgets are battery drains b/c all they really are is a monitoring app and if it is tied to something like FB or G+, then that data will be running constantly.

Examples:
Gmail = Enable (not enable/off b/c then it will keep your radio/data open)
Beautiful Widgets = Enable/off
mClock/Clockr = Enable/off
Angry Birds = Disable (with this and something like Adfree, no more ads in Angry Birds even though the ads are embedded in the .apk)
SMS/MMS = Enable or Do Nothing (why would you push disable)

Enable = Radio/data on when app is in use (front)
Enable/off = Radio/data on for background apps (when screen is locked)
Disable = Disables radio/data traffic completely when that app is running
Do Nothing = What is says.

I have been using JD+ for over a year on 3 different phones and have noticed a considerable difference in battery life, even on a crappy Motorola phone. Just takes some time to figure out YOUR settings and what YOU like. I have also used it on Stock kernel and had no problems either.