I have downloaded quite a number of these files (the zip files), extracted them, and consequently have thousands of these images. Each image is given a unique name.
I would cite them differently: I would cite the specific church book: parish (town and church name, if known), volume, type (eg, baptisms), specific page. Also include the name of the archive. I think the link for the film is optional (I have no opinion either way).
As far as creating a place to store them, I think consultation with the Zamrsk archive would be essential before anything is done.
What might be a better approach is to link to, or download the catalog of all the church books, provided there are no terms of service or copyright issues. Discussing this with the archive should also be done.
Note for Robynne: I have used resources at a number of the Czech Archives, and they have all been without cost.
Note to whom it may concern: the catalog is about 2500 pages, covers hundred and hundreds of towns/parishes, and there are many files per parish. The files are all quite large. Thus, this could take a lot of computer storage.