Personally I write my scripts similarly to a screenplay - I was formally trained in writing screenplays and have written stage productions before so it is just comfortable to do it that way.
I separate them by page indications and then the layout of the panels comes in the thumbnail sketch stage.
An example of how I format them (forgive me I just threw this together in like 3 minutes):
INTERIOR - DEATH'S DOOR BAR - LATE EVENING
(p1)
RADICAL JASON and FOREAS UNDERDOWN share a table with a few assorted criminals. JASON sips his usual choice of Ratten 1968 rum while Foreas stares absentmindedly into a glass of Pinot Grigio. They are playing a card game lazily, as S.B. approaches the table.
(p2)
S.B.
(close-up, st level) So, who's winning?
JASON
(confidently) Do you really have to ask?
(she grins at him and collects a couple of empty glasses)
(p3)
S.B
Well, you kids have fun.
(she mumbles the lyrics to "Little Lies" to herself as she returns to her position behind the bar)
FOREAS
(swirling his glass) You just didn't want to admit you've got a lousy hand, did you?
JASON
(frowning, leaning towards him with mock-aggression) Do you know how to spell "suplex"?
FOREAS
(stares at him blankly for one panel before responding) Do you?
JASON (off-panel)
Shut up.