Yes.

The aquabus can address up to four MPS devices (12. 13. 14, 15).
The two MPS 400 flow sensors will each take one address.
Assuming you are referring to the aqualis with built in level sensor, then two of those would take up the balance of the available addresses.

MPS addresses can be assigned in aquasuite under the system tab for each device.

The aquabus has four (4) MPS device addresses available.

If both aqualis reservoirs have the built-in level sensors, then the additional two MPS 400 flow sensors would max out the aquabus' MPS addresses.

You will still be able to manually control the two D5 USB/aquabus pumps with the USB connection.
Pumps are generally considered set & forget anyway, so that would be a viable option.

If you want the D5 USB/aquabus pumps to be integrated with the aquaero, then either the flow sensors or the level sensors would have to go USB connection only.

It appears you have six MPS devices, so you will have to select which four you want to integrate with the aquaero.