For students working on their MASTERS theses in Linz:
even though you work in Linz, you need to fill in the Assignment of master thesis and submit it in Budweis (Study Dept.) with all the signatures - this is needed for the subsequent uploading of your finished thesis. You can do this anytime during your study, but the simplest and best will be, if you submit the assignment as soon as possible; you will not need to think about it when you are finishing.
When you finish your thesis, you need to upload your thesis in the STAG system.
Bachelor students and master students working in Budweis - of course, you need to submit the assignment as well. The sooner, the better. And of course also upload your thesis into the STAG system.