Usually I have a fairly good idea of what a given patch needs to be. But then, I've been doing this a while.
Probably the best way to proceed is to start with a very simple signal chain: VCO -> VCF -> mixer. When you arrive at something that seems to suggest "add x" or "tweak y", then do so. Lather, rinse, repeat. As this process continues, you'll notice that the core sound you'd started with has grown in complexity, as has the patch itself. And while that sounds pretty simplistic, it does work; this is how I was taught to patch on my undergrad school's ARP 2600, more or less. Feed a VCO to the VCF, turn up the VCF's direct out, then start screwing around with that basic path by degrees. The other benefit of proceeding this way is that you get a really good overview of what the various modules can do, how you can make them behave in ways that work for you, and so on. Over time, you wind up with a really good mental picture of the synth, and you can patch pretty rapidly...and then going beyond that, you'll notice that you can structure the basics of a given patch in your head, before even picking up the first patchcord.
Takes time, though...like any other musical instrument, fluency implies practice.