They are both "big subjects" and need more study time than, say, either CT1 or CT3. So your first question is whether you have enough time to do these justice in the summer period (if you're only starting now, then that's just three months if you want to leave yourself the whole of september for revision). Whether 3 months is plenty, or not enough, for you, depends on you personally. But think about how long it took you to study for CT1 or CT3, say, and multiply by 1.5, and that will give you an idea.
I don't think there is any issue about content. CT5 and CT6 basically don't overlap. For CT5 you should have done CT1 already, and for CT6 you should have done CT3 already.
One more consideration. By end of 2018 you will need both CT1 and CT5 to get exemption from CM1; and you will need both CT4 and CT6 to get exemption from CS2. Do bear in mind!
As to "how to prepare" - I can only comment on CT5. But I think it's the usual advice. Get through the course material as quickly as possible (not worrying too much about proofs and derivations - eg don't feel you have to "show" every step of every theoretical development in the course) and then get on to practising questions as soon as you possibly can. Nothing, in my opinion, works better.
Hope that helps.
