Thank you very much. I will contact the services you have mentioned to see what they offer. For those who might find it helpful, I will share what I have learned so far.
Generally I was able to learn recently that everything is declared together in the following year with the tax returns - I believe this is a form that is submitted via ELSTER. For any income that can be deemed as exemptions I would still have to declare it on the returns form but also provide documentation as to the nature supporting exemption (e.g. that the scholarship is funded by a non-profit organisation and from public funds etc.) There are several items that can be deducted from taxes such as health insurance and pension payments, work related costs such as the purchase of specific items (e.g. laptop, charging devices, microsoft applications etc.). However I think speaking to a tax advisor might be helpful to identify these things.
After the tax returns are filed you would receive a communication from the Tax Office invoicing you for whatever you need to pay and they will also inform you payment details such as account numbers, method and deadlines. The deadlines I believe are usually lenient, as in if the amounts are large it can be paid in instalments.
I hope this is helpful.
Best wishes,