Congratulations on your new cellar! I have 2 Eurocaves (260 model) and have the same frustration that you are now experiencing. Over the course of a couple of years, I have finally found a decent system that works for me.... The top of one unit gets champagne and sparkling wines (2 shelves), the middle gets everyday white wines (2 shelves) and everyday red wines (2 shelves). Below this I put stuff that needs some time, but not a lot of it (2-5 year range) and pull it up as needed. These also work for special occasion wines. The very bottom holds magnums. The other unit is exclusively used for longer term (Bordeaux, Barolo, etc.) stuff and is arranged in no particular order.
As to software, we drink wine just about everyday and so managing it to a specific location has proved to be difficult. (If the computer happens to be right next to the cooler, that might be a different story). I use Cellar! software
Again, this works for me. Hopefully you will find a solution that works for your needs.
Cheers, Gary