Perhaps this is a rookie problem though.

-- merzky_shoom

I would say that it is. I made what I would consider a similar mistake, building my rack with an eye towards form over function at first to some extent. I still like to group many of modules by manufacturer, but I am mindful to organize everything in a functional way first.
If it comes down to it though, I'm not paying an extra $100 for a module that is aesthetically pleasing over one that has the exact same circuitry. I guess I'd prefer to have my modular all one color, but it's a patchwork because that's what made the most sense from a playability perspective.
Have fun!