Sort of depends whether or not the signal input through the multichannel analogue inputs bypasses all the digital processing in the amp. In some designs, such as the TAG McLaren Audio processor I use from time to time, the multichannel analogue input is a 'bypass' connection, just feeding to the output via the volume control.
In some receivers, however, the multichannel analogue input may be converted back into digital, punted through all the processing and then converted back to analogue for output, however crackpot that may seem.
So if you have an AV amp with multichannel inputs designed to bypass straight to the volume control and then the power blocks, you should use the player's speaker set-up; if the analogue signal goes through all the DSP, you shouldn't bother - the settings you already have on the amp will do the job for you.