I use Inkscape for my word balloons and lettering. It's a vector program and a free download.

What I do is import a PNG copy of my page, and set the document size to the size of the image. Then create the word balloons and lattering over the top of that. Delete the background image so I am just left with the lettering, and export is as PNG. Importing that back into my graphic program as a layer gives me the letting with a transparent background so my artwork can be seen behind it.

I create all my pages at print resolution, including the lettering, and only shrink it down for the web.

No, Photoshop. They need to work with the image so they're not necessarily placed on top of the art, I plan for them before I start drawing. I keep them on a separate layer nevertheless in case I ever want the pages without balloons.