The Bose speakers typically have a lower impedance (1.2 ohm to 3.2 ohm) than typical aftermarket speakers (4.0 ohms), and some aftermarket head units with built-in amplifiers may be overly stressed to maintain current flow to the Bose lower impedance speakers. If you use an aftermarket external amplifier, they will typically be able to power the Bose speakers without issue.
You can probably add an aftermarket head unit to an existing Bose external amplifier, but you will have to deal with Bose connectors, which are not standard. You may be able to purchase a connector conversion patch cord to match up an aftermarket head unit with a Bose external amplifier.
