It's tempting to think that you should pick one colour code to use forever. But that's not the best idea.
Firstly, as we already said, you should start small and then expand (if you want).
Secondly, you may discover that your chosen theme, wasn't a great choice (perhaps it's too similar to another topic). There's no point being bound by that past decision.
Finally, your interests, needs and what God wants to speak to you about will change overtime. You should not stick to what you needed in the past.
The difficulty comes in understanding an old colour code if you have changed colour codes. The simplest solution is to add a key at the front of a physical Bible and use that code for as long as you use that Bible. If you do change colour code, mark the page to show which code is being used.