I'm using two font sizes - one standard size and a smaller one (1-2 pt smaller) for muttering or background conversations. I wasn't really doing this before SPEJS though, so my comics had quite a font-size party perviously XD
I was really horrible with not planning in speech bubbles until maybe a year or so ago. Nowadays I'm trying to plan in dialogue in the thumbnails, and after I've scanned my thumbnails and arranging them for making a finer sketch, I usually add the text and speech bubbles so I know if I need to re-arrange characters and such. I would really recommend doing this so you have a general idea of where your speech bubbles will be and so on, it'll help you a lot in the end =)
As for making speech bubbles, I'm using the sppech bubble tool in Clip Studio actually ^^; I think it works just fine, and looks about the same, or even a bit better, than my previous approaches =)