They're still working on the Store. You're talking about downloading the XAP files for manual installation of apps. I noticed this feature is absent from the new Store as well... The only suggestion I have is to download them from third parties until they get the Store finished.
I had to do this with one of my games that just wouldn't download and install from the Store. Here's where I found the XAP file for Age of Empires for example:
Age of Empires: Castle Siege XAP 1.10.0.0 - Free Strategy & Simulation Game for Windows Phone - Appx4Fun
edit: while this might be a workaround temporarily, while we wait for the issues for the store to be resolved, always approach these third party sites with caution, as they can sometimes be shady. Always use these third party sites at your own risk! None of us here, including myself, can be responsible for anything you download from an unofficial source. The above site that I linked was again, just an example of said workaround. The safest bet, is to wait until the unified store is finished.