One thing to keep in mind is that even though a receiver has two subwoofer outputs, they may not be independently configurable. A lot of times, the two outputs are paralleled. When you read the manual you find you can only do one configuration and the results are sent to both subwoofers. This can apply even to expensive AVRs. For example, NAD's flagship AVR the T778 falls into this category.
I have been using Marantz SR series AVRs for many years. I had an SR7008 in my main system until I replaced it with an ARCAM AV40 Pre/Pro a couple years ago. The SR7008 was moved into the living room system. The SR7008 has two subwoofer outputs but they cannot be configured independently. Most of the SR series receivers have been replaced with the Cinema series. The only SR still available is the SR8015. It's subwoofer outputs are independently configurable as are Cinema 40 and Cinema 50.
ARCAM: the AVR20, AVR21, AVR31 as well as the pre-pros AV40 and AV41 allow independent control of multiple subwoofers through Dirac Live Bass control. However, while a Dirac live license is included with the unit, the bass control software is a separate purchase from Dirac Live with the multi subwoofer version costing $499.
I prefer the ARCAM AV40 pre/pro (the AV41 is the latest model) to the AVRs for two reasons. First, I prefer balanced connections and the pre/pro has both single ended and balanced outputs while the AVRs only have single ended outputs. Second, I connect the AV40's main speaker outputs to one of the inputs of my two channel preamp that I configure for HT by-pass which allows me to use the main power amps and speakers for both music and HT. This means I only need amplification for two surround channels and I'd rather put the money into two separate amps than pay for five amplifiers that I wouldn't use with an AVR.
Denon: The AVR-X3800H, AVR-X4800H, AVR-X8500HA, and AVR-A1H all have independently configurable subwoofer outputs. While I've had Denons in the past, I preferred the sound of the Marantz SR series receivers so those are all that I used until the ARCAM AV40.
I only know of Anthem by reputation never having heard any of their products. Their MRX540, MRX740, and MRX1140 AVRs all have multiple independently configurable subwoofer outputs.
Mike