I see that all submissions have a web player with their game but no PRG file to avoid publication before the contest ends. I know how to add the web version, but how is the game submitted then? Should we send the PRG-File via a separate channel?

I think the safest bet is to submit the prg via email as in the rules, I initially put my entries on the web player because I thought it was a shame if no-one could play until April, and also thought it would help generate interest. Jamie the competition organiser was fine with that, but eventually all entries will need to make their way to Shallan in .prg format so he can test them against the rules. I haven't actually submitted the .prgs yet in case there are bugs or improvements I can find before the deadline.

The way I submitted an entry is to first upload the web player and link to the competition then email the prg, d64 or whatever it is to the competition organizers - to prove that you are interested in submitting the entry to the competition.