on the rear of your marantz you'll see preouts for all seven channels--you connect the power amp (using red/white analog cables) to the preouts marked front right and front left, respectively. your manual will show you the exact location. you will then connect the front right and left speakers cables to the power amp, not to the avr (the other speakers, which are powered by the avr remain connected to the avr). after connection, you'll redo your setup, level balance etc. to adjust speaker volume and so forth.
there will be no problems switching between music, movies, tuner or whatever--the only difference is that your front speakers aren now powered by a different (presumably better) amp than the rest of your speakers, which will only be discernible in two channel mode.
again, i'd do some comparison to the sound with or without an external amp to see if it makes a significant difference in your case. i added an external (parasound) 2ch amp to a denon 4800 in my bedroom system and found it made a huge difference, but having not heard your marantz avr i honestly can't opine as to your setup. good luck and let us know how it fares.,