How can Madara Uchiha use Susanoo when he does not have 2 mangekyou abilities in his eyes?
First of all, it is not mentioned anywhere that Madara doesn't have two Mangekyou abilities in his Sharingan. It is simply not revealed just like Izuna's Mangekyou abilities.
Second, as mentioned on the Wikia,
Once a user awakens the Mangekyō in both eyes, or the ability of both of their eyes, they are able to perform Susanoo
it is not necessary to have any abilities specific to their Mangekyou Sharingan in order to perform the Susanoo.
First of all, the rinnegan is an improvement of the sharingan it self, so by having a mangekyou and the rinnegan, he would be able to invoke susanno. But the susanno is in fact a skill that can only be summoned while having two eyes, rinnegan and mangekyou. Sasuke have a rinnegan and mangekyou and is able to summon it.
Regarding the tsukuyomi and amaterasu I can't tell for sure. Right eye has the amaterasu and the left one has the tsukuyomi. I believe that Itachi explained this like this, but remember that kishimoto left some plot holes so we can't really be sure. Also, I think Sasuke used the amaterasu and the tsukuyomi while having only one mangekyou and one rinnegan.