Hamsters prefer most of their habit type things at floor level - eg house, wheel and toilet. Particularly the house which is best if open underneath and on top of a good depth of substrate - so they can do normal behaviours like burying hoards under their nest. It's probably why she is staying at the bottom as if a house isn't big enough to build a big cosy nest, or if they can't fit hoards under the next, they sometimes just make an open nest in the substrate under a shelf. Plus they like to be near their wheel!
Ideally they need one larger ground level floorspace although a shelf or level is good for putting a food bowl on and extra toys. Tubes and tunnels work best as floor toys really. As CMB said also, hamster tubes aren't always big enough. Our Syrian grew quite large and actually got stuck in some tubes. Even if they're not really large they can still get stuck if their pouches are full. Rat sized tubes make good toys for Syrians.
Ideally one larger cage is better than two smaller ones joined together as that doesn't give the continuous floor area so they can make their own habitat in it and use all the space with normal habits. It's better to have something lower and wider than something very tall with lots of levels as then there can be fall risks and they do like the floorspace and substrate which is a kind of terrain for them where they can forage for bits of food (if you scatter some), dig etc and they like moving substrate around as well to keep themselves cosy or just for fun.
Not sure how big your second cage is - but one larger cage with open floor space would be better. Something like the Alaska, Barney or Alexander from Zooplus are good, or the Hamster Heaven - but the Hamster heaven works best without all the tubes and plastic shelves, so you can fit a large enough wheel in (28cm diameter is a good sized wheel for a syrian).
The Alaska cage and Hamster Heaven have nice big front opening doors too, so it's easy to interact with your hammy.
Alaska Hamster Cage | Free P&P on orders £29+ at zooplus!
The Barney comes with a really good house and shelf so you only need a wheel and some toys.
Barney Pet Cage | Great deals at zooplus!
Same with the Alexander
Alexander Small Pet Cage | Available at zooplus!
Savic Hamster Heaven Metro Cage | Great deals at zooplus!
I have the Barney cage for our Syrian. But an Alaska is a good basic cage for a Syrian although it needs a house.
You have to be a bit careful with toys too - most toys sold for hamsters are too small for Syrians and only suitable for small dwarf hamsters - anything with a door or opening needs to be about 6cm in diameter (5cm absolute minimum). For a large Syrian at least 6cm diameter. How much does your hammy weigh? Gives an indication of size.
It's difficult if you've just bought a second cage - but if it's very recent you could ask for a refund, depending where you got it from. A number of members have done this when being sold a cage that wasn't suitable or big enough.