When it comes to the issue of vitamin B12 vs B complex, both types of vitamins are crucial. If you're lacking B12, consume more of it via supplements or food. If you're lacking vitamin B in general, consider B complex vitamins instead. Overall, both vitamins are essential nutrients.
So, the fact that your urine looks like a highlighter does, indeed, mean you are taking in more riboflavin than you need. But it's a no-harm, no-foul situation, as your body has a ready mechanism for draining the overflow. As a result, you needn't worry about excess amounts lingering in your system.