Your idea is commonly done. The two ends of the battery and an "artificial ground" from the 5 V regulator output. All analog signals will be referenced to the 5 V level. If you use AC coupling in and out, the analog signals can be referenced to the - side of the battery which is also the ground of the digital circuitry.
Well i guess you mean how to use the op-amps which need dual power supply ,well for this case there is some ct. which makes dc-dc converstion so some ct take the 9v and converts it to +4V , -4V and GND ofcourse