You can use your apple account balance to buy anything at the Apple store, brick and mortar and online.
However; their online store is a mess when it comes to using your Account Balance. I tried pre-ordering an iPhone and missed my pick up window on launch day due to the website bugs.
I ended up paying for my instore pickup with credit card; then when I went onsite to pick it up I asked the genius person to refund and rebuy the phone with my apple account balance. This worked for me when it failed miserably online.