I don't think it's necessarily about time management - there's not much point in spending time writing a thesis when you don't have many results!
But, now that you are in your third year, you need to see exactly what you need to do to finish your thesis and make sure you work towards your deadline.
Repeat things if you can or if you really need more replicates, but you can always just say in your thesis that you recognise that you should have done this or that.
6 months for writing up is fine if you have only writing to focus on. If you will still need to do lab work, or you will working part-time, then you will need a longer writing up time. I would say once you have a thesis plan, get the lab work done before starting serious writing.