Tipping in Prague

it is not a big issue in the Czech republic, 10% and no more is perfectly acceptable but only if the service is good,if just buying a coffee or a beer just round the bill up to nearest 10 crowns, so if a beer cost 45 crowns I would not expect change from 50.
taxi driver again just round it up but 25-50kc is considered a reasonable tip ,tipping though not expected is appreciated.
In some places especially in tourist areas servers will say Tip not included in bill and sometime they write this on the bill , this is illegal but does go on.Some place will have a cover charge, I have only had this in a few places and it is usually a very small amount 10 or 20kcs.

We have reserved a long-haul shuttle (Prague to Vilshofen). The fixed price is 224 euro. It is a car with driver ( i.e. Not a shared bus or van). I have a balance to pay at pickup of 4000-czk. We weren't planning to tip. Would that be correct? If not what additional amount?

I wouldn't tip. maybe give a 100kc or so if the driver has been helpful with bags etc.

To answer the OP:

You round up at restaurants and in taxis. For instance, a restaurant bill of 261czk would become 280czk. A taxi ride of 113czk becomes 120czk. An important part of the tipping custom here is that you tell the waiter/taxi driver how much to take when you give them the cash/card i.e. they tell you the price and you tell them how much to take. We do not leave tips on the table afterwards, but include the tip at the moment of payment.