Yeah, you can go either way. I wanted to use the Gmail client for my gmail because I like the layout of conversations better, though I like the htc notification icon better.
To stop notifications in the HTC mail client, make sure you're looking at your gmail inbox then press the menu soft key, select 'More' and the 'Settings' and then 'Notifications'. There you can turn on/off the sound notification and the notification bar/icon.
I ended up removing my gmail from the the HTC app altogether, just to avoid duplicate data, and it seemed like it wasnt syncing read mail all the time.
You can disable notifications in the Gmail client instead, if you prefer.