I just stacked a 9" & 6" round, both were layered with ganache & covered with fondant within an hour, in the time it took me to decorate, I stacked, but Im just a bit paranoid because I stacked with mcdondalds straws for the first time as opposed to thick wooden dowels.. The bottom cake is a bit on the soft-side
The cake needs to stay like that for 2 days so I'm not sure if I should dismantle it and put it together again later?

Why is the cake finished two days in advance?

If I were you, I would replace the straw with dowel. If you gonna be eaten the cake today, I would say it's should be okay. Two days seems too long for a Mc Donald straws.

I like to store my cakes in the frige--very well wrapped though for that length of time.

Cake is finished 2 days in advance cos I had no idea I was actually going to get it finished that soon!
They're muscakes and they last quite a while, in fact I think their flavour peaks on the third day.
If it were a soft white cake I'd be concerned.

You said the bottom cake is soft, so in that case I'd probably dismantle. If it were a firm/heavy cake then it might be fine.

(PS re: the two day thing...some recipes are actually better left for a couple days before eating. The mud cake recipe I use is one of them - I can leave it out on the bench for a week or more and it's still absolutely perfect. So having the cake made two days in advance is not necessarily a big deal)

How soft is too soft to leave it stacked?
It's a white mud but it is a bit more sponger than the choc mud which is the top cake.
It's been nearly 12hrs stacked and still seems ok. It needs to see us through another 29hrs...