Multiple Powered Up trains on 1 Bluetooth controller?
Each train needs the following two components:

Hub
Train motor

I'll assume you purchased a second set of these to convert your 9V train with, since you're asking how to control both trains using the same remote.
The LEGO Powered Up team has provided an FAQ for Powered Up which contains instructions for how to pair multiple Powered Up Smarthubs with one remote, on either the same channel or different channels:

How can one single BT remote be used to control multiple receivers or switch among them? Will this be possible in the app?
You can link up to 5 devices (Smart Hubs or Smart Controllers) together.
To create a network you first need to connect a Samrt Hub [sic] and a Smart Controller.
First Hub connection
Turn Hub and Controller ON by pressing their green buttons and they will link. The LED will blink white and then shift to same channel color e.g. blue. You can now change the channel color by pressing the green button on the hub and toggle through the 5 channel colors. When turning OFF the Hub or Controller the last connection is remembered and re-established when turning both ON.
Adding Hub to network
With the first Hub and the Controller ON and connected you can add extra Hubs to the network by turning the new Hub ON and then press both green buttons simultaneously on the new Hub and one of the components in the network (Hub or Controller). The new Hub is now added to the network with the same channel color as the currently selected channel. Again toggle to another channel by pressing the green button on the Hub. When more Hubs on different channels are added to the network you toggle between the different channels by pressing the green button on the Controller.
Note: The current Powered UP app supports control of a single train.

Note that when you have two Smarthubs paired with the remote on the same channel, when you press a speed control button on the left side of the remote, both Smarthubs will respond. This is shown in a video by HispaBrick Magazine. This means you'll start both trains concurrently with a single button press. To avoid this:

Change the channel on one of the hubs by pressing the green button once. You can then switch to this channel on the remote by pressing the green button on the remote, and cycle through all 5 channels back to the other hub to control that other hub again.

Or if you want to be able to control each hub independently using each side of the remote without having to change channels on the controller, simply switch the plug on one of the hubs to the other port while both are still paired on the same channel.
The second port is typically used with a different device such as a Powered Up LED Light which you can install into your Passenger Train and you'd control the train motor and the LED light independently; however, it's not possible to have both motor and light controls and control two independent trains all on the same channel.