I can't answer specific details for your setup, but (with apologies if this is all obvious):
The function of your Amp is to power your speakers, which require relatively high power (watts) and high current (amps) analogue (continuously varying) electrical signals. This section is called the power amplifier (makes the power bigger - see?) and there is one power amplifier per speaker. To use these with multiple sources, it includes selection from multiple inputs and conversion of many input formats to the seperate analogue signals required. This part is called the pre-amp. Being an AV amp, it also selects and converts video formats for delivery to your screen, but there's no power amplifier for them.
Digital signals don't degrade; analogue do, so keep everything digital right up to the amp if you can. Even more so for amps that perform speaker and room equalisation in the pre-amp. They will convert everything to digital anyway.
You are extremely unlikely to damage your amp or speakers by selecting higher frequencies/resolutions. Most likely it will simply ignore the input if it can't accept it. The most likely way to damage your speakers is to turn the amp up to max with no input because you can't hear anything; then switch the input to something which the amp can process.