I actually use both because there are some benefits to using the HTC mail client, such as copying text, but for the most part I use the GMail app because the HTC mail app doesn't have push for Gmail, so it would kill battery. To turn off the notifications on the HTC mail app, just go to menu>more>settings>notification settings, and then just uncheck all of the options. Then you won't get the HTC mail notifications.
On a side note, if you are using the GMail application, you may also want to change the Send and Receive setting to manually update only when you go in to the HTC mail app. Otherwise it will periodically check depending on the frequency you set, which will take up battery.
