When aligning objects with the Align panel, you can set one object as the reference by clicking on it again after you've selected two or more objects. The reference object will then get highlighted, so you know what the reference is.
Is that what you're looking for?
Also, keep in mind that in the Align panel there are some options to control different kinds of alignments (Align to Artboard, Align to Selection, Align to Key Object).
If that is not what you want, please clarify a bit.