In your situation, as you appear to realise, you are liable to German VAT as well as any import duty that may be payable. The position is reversed if German or other EU buyers purchase from your .com store in which case the liability is theirs.
The simple answer to your question is that you should normally be able to have these charges billed to your Fedex account by ticking the box on the AWB marked Bill duties and taxes to Sender, but check with Fedex that it’s OK for you to do this. This facility is only available when shipping through Fedex and other major couriers, not postal shipments.
The standard VAT rate is 19% (20% in the UK) which is liable on the CIF value and duty combined above the threshold limits below which these taxes do not apply. You will need to make your own enquiries about VAT and Duty thresholds which vary from country to country - in the UK it is £15 (invoice value) and £135 respectively.