It can be confusing - no doubt about it, but the Forum has a lot of information by using the Search function.
Conventional engines need a transformer with a mechanism (like a handle) to vary the power (voltage) to the track to be able to speed up and slow the train down. OTOH, command controlled engines like Legacy and TMCC require a constant 18 volts of power to the track if you want to run them under command control. So, generally speaking, you can't run both kinds of engines on the same track at the same time. Note that you can run a Legacy or TMCC engine conventionally, using a conventional transformer (see below) but you will not have access to all of the engines Legacy/TMCC features.
The 6-85226 Powerhouse supplies a constant 18 volts to the track - the voltage is not variable, so you cannot use it if you intend to run conventional engines - it is designed for running command controlled engines. In order to run conventionally, you would have to get a conventional transformer like an MTH Z-1000 or a Lionel CW-80. As above, you can run a Legacy/TMCC engine with a conventional transformer.
The 990 Legacy system is used to control Legacy/TMCC command controlled engines. The 990 base does not supply any power to the track - it only supplies a signal to control Legacy/TMCC engines. The power to the track is still supplied by a power supply like a transformer or Powerhouse.
It can be a hard concept to grasp at first, but think of it this way - command control engines require about 18 volts to run properly, whereas conventional engines run best at about 10-12 volts. Therefor (for all intents and purposes), you cannot run a command control engine and a conventional engine on the same track at the same time because if you set the transformer voltage at 10-12 volts for the conventional engine, the Legacy/TMCC engine will not operate correctly and if you set the transformer voltage to 18 volts, the conventional engine will fly off the track.
Even though hooked up to the layout, the 990 base signal does not interfere with the conventional operation. If you want the convenience of being able to run conventional engines using the 990 remote, then buy a Powermaster (not Powerhouse) and integrate it into the system using the 6-12893 cable. It allows you to vary the voltage to the track for running conventional engines using the 990 remote, much the same way as if using transformer handles.
Hope this helps.