Actually I find Photoshop so efficient I can't imagine using anything else. For me a page will have these layers:

One background
One layer per panel (usually not more than four per page)
One hidden layer that I use as an aid when composing dialog
One layer for all balloons
One layer for all text boxes
One layer for each text (number depends on page)

That's typically less than 20 per page, depending on the density of dialog.

Trying to write text over balloons is the wrong way to do it. I write the text first, then draw a path round it, and fill the path on the balloon layer. That way the balloon always fits the text perfectly with no wasted space. One can get very neat results with very little effort.

Also I always render to the size of the panel, so I never need to resize.