Get it clear in my head

I've been writing for a long time so I know what it means when a story isn't coming together. The same goes for an article.
It means it's time to reboot and start all over again with a new approach.
I've hit a wall with the article I'm working on. I can't get past the opening paragraph. This used to happen some times when I was working on essays for uni.
It still happens occasionally when I'm creating a novel. I'll get up to 20 000 odd words and then realise I've got about three or four subplots going on and no real plot or way to reconcile any of them.
I need to get my arguments clear before I start writing. My head's a little messy about it because I've got three different points or arguments to make within a small space. I have to clear about what I'm saying and what message is the most important.
Oh the joys of being a writer.
It's never as easy as it seems is it?