So, the latest build will automatically assign double bonds, so that when you start editing the structure, it is much easier for Bioclipse to keep up with what is going on, solving all sorts of corner cases. (A good alternative name for cheminformatics would be cornercasinfomatics :).
I stress one more that if people would just say what they meant, all these things were non-issues. It's really the scientist messing up, and Bioclipse (/CDK) has to figure out where he messed up. I still have a very strong opinion on have your cheminformatics making assumptions just because the scientist has been lazy. That is just the world upside down.
One last reminder: you can switch the rendering between aromaticity rings and normal double bonds:
So, with that 'Show Aromaticty' unchecked, you can depict structures like this:
Actually, as you can see in that Preferences page, you can set a lot of rendering options. The JChemPaint rendering stack is very tunable. We have long wished to use a CSS-like format to share such settings, but never gotten around to that yet. Someone interested?