After installing TexnixCenter and MikTeX as part of the Protext package, users may encounter difficulties viewing documents in PDF or PS formats. The recommended applications for viewing these files are Adobe Reader for PDFs and GSview for PS files. To generate the output, users should select the appropriate option from the drop-down menu in the interface, which includes LaTeX to DVI, PDF, and PS. The key step is to find the 'build output' option, which compiles the document and opens it in the selected viewer automatically.