There could be many factors that could cause imperfections in the appearance of your fondant covered cake after it sits for awhile. So, without knowing all the steps you did in how you filled, frosted, and put on the fondant it would be hard to help you with that.
As for the boxing situation, I answered a post about that some months back. I use regular bakery boxes by altering them a bit and using clear plastic film. How I go about it is I figure out how tall my two tier cake is, including any toppers, and then add another 1/2 - 1". That is the height my box needs to be. Take the bakery box and measure the height of the bottom edge (usually 6" on my boxes) and subtract that from your total height. That then is the additional height you need. I then measure that amount continuing on up the box onto the lid portion. I mark the measurement on both sides of the box then cut the flaps at those spots. I then crease the new "lid" portion. Now, tape the sides together to secure your now partially upright overhang lid. You will no longer have a lid that will close. Instead doing this creates a "view window" for your cake customer to see without having to unwrap the cake right away. I cover the space between the overhang lid down the front of the cake to the front bottom of the box with the clear plastic film. I then wrap the film similar to a package nice and tidy and tape the sides securely. I place my business logo on the front of the bottom of the box before placing the plastic film on the box. This method of boxing looks professional, does not cost any extra and is perfectly secure. I have delivered many two tiered cakes this way with no mishaps. I have even done it for boxes up to 16" with no issues. HTH