Applications such as the Software store are not aware about drives, they only see the filesystem locations. Where to physically write the bytes when you save files or install programs is done by the Linux kernel, transparently to the rest of the OS.
To combine multiple drives you mount the partition from one drive onto the filesystem at the given location that you want. To "mount" a partition means to make it available to the filesystem at said location. When the computer boots, you need to configure it to tell it to search for the drive's partitions and mount them automatically for you.
Just to clarify, this seems like a different topic. A repository is a remote server you download files from. It's not related to where in your machine these files are stored. But as I said, this isn't an issue since all the real work would be done by the kernel.
Take a look at this thread for a similar scenario involving multiple drives: