I'm still not 100% sure if I understand, but if I do understand, this is the best advice I can give you. First thing, make sure you have at least the basic storyline written out in longhand. If there is certain dialogue you know you want, write that out too and put it more or less where in the story you want it to go. You can even get adventurous and write out the whole thing with just actions, descriptions and dialogue without breaking it up into panels and pages. It's much easier to make the panels and pages if you can break up the material that exists instead of trying to craft it a panel at a time. It's easier to know how to get where you're going when you know where you're going. Find the first panel, find the last panel, it's much simpler to find the panels in between them.
John wakes up. John gets out of bed. John walks into the bathroom. John gets into the shower.
John - I hate Mondays.
In script form, this could be several panels, or just a couple. This could be an entire page, perhaps even more, depending on how you break it up later and how you want the story to read. I couldn't possibly tell you how best to break it up, that's all down to personal choices as a writer, and how you want the individual story to flow. Sometimes it works to drag it out, sometimes you want it move more quickly. Figure out the essence of what you want the work to say, then say it. Sounds really oversimplified, I know, but a lot of writing is just that...you fill in your own blanks. It's like Lego, you use the pieces you need to use to make what you want, you cast away the rest, and the only thing that decides which is your own vision. Later, find an editor (someone you trust to tell you the truth without being overly nitpicky, preferably someone who knows how to tell a story themselves) to help you figure out how to refine it.
Try doing something called thumbnails. Thumbnails are small, sketchy versions of the comic page. Do as many as you need to do to get the visuals straight while getting across the information you need to get across. Don't worry about the art being good, don't worry about details, all you need to worry about is basic figures and objects, blocking, where your word balloons will go (if any) and what words will be in them. A lot of artists who have trouble making their own scripts do this, and a lot of writers do it to help them get a visual feel for how to describe the script.
If you've done this already or if it doesn't help and you still have the same trouble, then I'm not sure what else to tell you. Like I say, I might not understand exactly what is the problem, or you might just not be very good at storytelling and may want to consider finding a writer with whom you can work.