Regensburg Central Station FlixBus to Prague

Google shows it to be at 16 Bahnhofstrasse. Google Streetview shows a bus stop sign there that says "Fernbus", which is German for long distance buses. There is also a schedule board there with a Flixbus poster on it. Here is a shot from Streetview.
https://www.google.com/maps/place/Flixbus+Bushaltstelle/@49.0125414,12.0975498,342a,15y,187.39h,78.15t/data=!3m7!1e1!3m5!1sHjOx3_793lAkgGipc1w6SQ!2e0!6shttps:%2F%2Fstreetviewpixels-pa.googleapis.com%2Fv1%2Fthumbnail%3Fcb_client%3Dmaps_sv.tactile%26w%3D900%26h%3D600%26pitch%3D11.848020363721474%26panoid%3DHjOx3_793lAkgGipc1w6SQ%26yaw%3D187.38593255632466!7i16384!8i8192!4m7!3m6!1s0x479fc1a4c18eb9ed:0x2d4992feea9c2835!8m2!3d49.0124828!4d12.0973311!10e5!16s%2Fg%2F11g4j64wmv?entry=ttu&g_ep=EgoyMDI2MDYxMy4wIKXMDSoASAFQAw%3D%3D

Leaving the station building turn left and walk into Bahnhofstraße towards Parkhaus (car park) Dallmeier. The Flixbus stop is right in front of it (as Sam says, the stop is just generally marked as a ‘long-distance bus’; Flix would have to pay for its own sign, and they can’t be bothered to do that).

But like I said, there is a Flixbus information poster in the glass-enclosed signboard at the stop which you can see by zooming in on Google Streetview.

There's a train, though. Why would you take a bus when there's a train available? Departs every two hours, no change.

Viking is your friend here. A day or two before you leave tell them where you want to go and what time you want to leave. They will arrange for a taxi to take you there. I would recommend taking the train. We did, from Regensburg to Munich. Very easy.

Also, you really want to take a taxi to the station. The boat docks in town, but the walk, with luggage through the winding cobblestone streets is not as much fun as you think it might be.