1) Trust your gut - set your speakers to "large" at the player and "small" at the 990. This will disable the player's bass management for any analog outputs. It won't matter for the player's digital output, since that output would not receive any bass management at the player.

2) There is a bug (which I've been told is slated to be fixed by the firmware update that's in development) that causes audio inputs to disregard the subwoofer trim setting. If you have your sub trim set to a negative value and your two-channel sub offset is still at zero, you may see this as a louder sub in music. One option is to apply some two-channel sub offset (which is what I'd recommend); another is to calibrate the sub so that the 990's sub trim is zero.