I am doing a two tier wedding cake. I plan on covering each tier in white fondant, and doing black fondant pinstripes, with flowers draping from the top down.
Now, I have never done striped on a cake, so I have a couple questions.

Is it easier to stack the cakes, then apply the striped, or should I stripe them and then stack them?

And then applying striped to the round cake, when applying up the sides and across the top, will the stripes crack as they are being folded across?

ALSO (sorry!)

I am making a vanilla and chocolate cake, alternating the layers, and filling it with Bavarian cream and chocolate ganash. Obviously, fondant on a cake doesn't really do well refrigerated, but the cake will be made two days before the wedding. How should I be storing it? I'm concerned about the cream in the custard and ganash. Usually I refrigerate my cakes and decorate them day off, but I absolutely have no time to do so this time as I am in the wedding party as well.

Any help is appreciated

......making a vanilla and chocolate cake, alternating the layers, and filling it with Bavarian cream and chocolate ganash....fondant on a cake doesn't...do well refrigerated,....How should I be storing it?...

Sorry I can't address your ?s on pinstriping but this I can answer.
It will be fine at room temp. Just put it somewhere out of the way where no one - human or animal - will not bump into it or tamper with it in any way.
It will be just fine - unless it is over 80 degrees in your house

I do pinstripes alot ...

1) Is it easier to stack the cakes, then apply the striped, or should I stripe them and then stack them?

- I always add stripes then stack them because it helps me make the stripes perfectly even. However if you think you may mess up the stripes while stacking your cakes - stack them first, then add stripes last. Just be sure to measure the distance between each stripe well

2) And then applying striped to the round cake, when applying up the sides and across the top, will the stripes crack as they are being folded across?

- Nope, I just use a claygun and it works great. Just make the stripes with the clay gun as you need them (right before you apply each stripe to the cake) so that they don't dry out and crack.

3) I am making a vanilla and chocolate cake, alternating the layers, and filling it with Bavarian cream and chocolate ganash. Obviously, fondant on a cake doesn't really do well refrigerated, but the cake will be made two days before the wedding. How should I be storing it? I'm concerned about the cream in the custard and ganash. Usually I refrigerate my cakes and decorate them day off, but I absolutely have no time to do so this time as I am in the wedding party as well.

- Definitely keep it frigerated. I always store my decorated fondant cakes in the frig and never have a problem. (I use Satin Ice Fondant) Plus when it's frigerated, the cakes are alot more stable/solid for delivery.