There are a few different ways that Czech libraries organize their materials. Many Czech libraries use the Universal Decimal Classification (UDC) system, which is similar to the Dewey Decimal Classification you may have seen in American public libraries. Some libraries do choose to create their own classification systems, to reflect their library's collection. Sometimes the system can be confusing to interpret; you can always ask a librarian for help in locating what you are looking for. In many cases, the library's stacks are closed, so the librarian will bring you the item you are looking for anyway.
Many libraries in the Czech Republic, including most major public libraries in urban centers, have an online catalog system, like UNC-Chapel Hill's Library Catalog, for which the search terms are similar: title, author, subject, etc. However, many catalogs from smaller libraries, including some university departmental libraries are still not accessible online, so a card catalog system will still be in use. Again, you can always ask a librarian for assistance.