So I'm making a unicorn cake with pastel colors this weekend for Sunday 10/21/18! But I plan on baking the layers tonight. I'm using boxed funfetti cake mix and two 8x3 cake pans! But I've noticed in the past that when I bake cakes in these deep pans the center of my cakes tends to fall, which ultimately means that I sometimes lose more than a little cake in the process. Can someone tell me why this happens? 

Also! 

1. How deep should I be feeling a 3 inch deep cake? I usually fo about 2/4 of the way, or about halfway. But perhaps I'm pouring too much batter? 
2. If anyone has a funfetti cake recipe that would work better instead of a box I'm willing to hear it! I know for stacking cakes you need a pretty dense cake and box cakes make some really loose fluffy kind of cakes? c: Thanks in advance! Wish me luck, I'll post photos when they're done! 

I usually fill my 3" cake pans halfway.  A box mix will do just fine for the two layered cake you are making.  I typically use the WASC cake recipe to doctor my box mixes up a bit but it certainly doesn't make a super dense cake and I do not believe that a cake needs to be dense for stacking.

As for why you cake is falling it could be the temp of your oven.  Even if the dial says a certain number your actual oven temp could be off so I would invest in an oven thermometer.  You might be slightly under baking your cakes.  A 3" pan needs to bake longer than a 2" pan and the times given on a box mix are most likely for a 2" deep pan.  Also, yes the toothpick may come out clean but that doesn't always mean that the cake is done.  I use a cake tester but I also tap the top of the cake and if it springs back then it is done, if not then it needs a bit more time in the oven.  I also may be tempted in trying a different cake mix brand to see if that may help as well.

My familiarity with boxed cakes is limited, but these suggestions might still work for you.  Filling 1/2 to 3/4 is fine for most cakes.  The two main problems you will find when your cake sinks in is:

1.  Oven too hot.  Too hot and the cake baking powder will react quickly and the structure of the cake cannot sustain the quick rising and it can fall in on itself.  For the majority of my cakes with baking powder, I bake at 330-335 F.  Usually takes a bit longer, but I prefer the lower temp and mine do not fall or dome up.

2.  More common for homemade cakes is after the sugar and butter are creamed on high, the rest of the ingredients should be mixed in on low speed.  If they remaining ingredients are mixed on high speed, it will whip more air into the batter and the same problem will occur.  The cake rises too quickly due to the air bubbles, but the structure cannot take it.  If you are making the cake mix with a mixer, then low speed would be all you need, or just stir them together by hand.  You (typically) are not trying to whip any air into most butter cakes.

Hope this helps.

I just make a basic white cake and mix sprinkles in for a funfetti cake. Just mix the sprinkles in at the very end. 

Here is the link to one of my favorite white cake recipes.

https://www.mycakeschool.com/recipes/almond-scratch-recipe/

I also never fill my 3" deep cake pans more than half full. Mostly I don't like baking in a pan deeper than 2" because at my altitude the deeper pans just don't work out as well.