Backgrounder can be backgrounded by setting an override in the Backgrounder preferences application. Set it to the "Backgrounder" backgrounding method to run it as if it's in the foreground, and set "fall back to native" off. You'll want to also set "enable at launch" and "stay enabled" to on for the following reason...
The only reason you can't "activate" Backgrounder in Cydia is because the developer of Activator, the method by which you bring up any mobilesubstrate program that can be brought up, basically, felt he should disable Activator controls in Cydia for "safety" reasons or something. This is totally unnecessary. SBSettings, Backgrounder, and all your other mobilesubstrate programs are still running, but because Activator prohibits actions in Cydia, it is not possible to call them up. By setting enable at launch and stay enabled to on you can at least bypass this bs with backgrounder. For SBSettings and all other mobilesubstrate programs, you will not be able to access them in Cydia, but this shouldn't matter because you can simply leave Cydia in the background and go do whatever. I do this... no problems whatsoever. Also, Activator didn't always used to be this way... not too long ago you were able to 'activate' any running plugins from within Cydia... Now you cannot.
Hope this was helpful
Xanadeath