Kat--If I am playing with a group and need to make the melody stand out above a background, I use a medium pick. When playing solo I use the thinnest flatpick I can find. Much less pick noise, etc. Strumming with bare fingers is good for accompaniment, but I can't do much to boost melody that way. Banjo picking, three-finger style, would definitely eliminate overkill on sound level.
One further thought: I finally found the correct strings to use--after driving two instrument gurus to drink--and strung my second "laptop" to G-D-G instead of D-A-D I started with. Much mellower sound.
I've gotta respect what Bert says about the problem being mainly on the hardware side, though. Somebody with recording expertise would probably solve 90% of the problem without you changing anything.
CC