You still want to use the receiver's x-over rather than the sub's. The x-over on the sub only affects the sub itself, not the other speakers. Most subs have outputs for the main speakers, so you would connect them to the sub rather than the receiver. In a case like that however the x-over still does not affect those speakers. When subs have outputs like this, it will have a fixed x-over, often at 80Hz, so this basically doesn't buy you anything over what the receiver already does and lacks the flexibility to adjust it as the receiver does.
Try this: set the receiver's x-over to 80Hz, use the LFE input and then turn the sub down until it blends smoothly with the Bostons and does not call attention to itself.
The A26 lists a -3dB (roughly the bottom useful point) of 51Hz, so it should work well with a 70 to 80Hz x-over, allowing the sub to be crossed lower to aid in reducing your ability to locate it. It sounds like volume of the sub is the issue here though, not the x-over.
When you are listening, what "mode" are you listening in? With only the two speakers, you should always have the receiver set to Stereo and the receiver should also be configured not to use the other channels for other types of signals.