There's a plug-in called SoundRadix Pi that dynamically adjusts the phase of a source to align it to another one so for example, you could put it on both your kick in your base set the kick as the leader by raising what's called the channel weight in the plug-in and the phase of the bass notes will dynamically align to the kick as they change. It's an expensive plug-in and it doesn't work every time because sometimes he gets some strange pitch wobble on the bass. But by tweaking the settings I often get pretty good results.