Subwoofer Out VS Subwoofer Crossover

You can still set the sun low pass filter lower than 100 Hz if you want.

You can use your sub with the 701 the same as with your other integrated or you can use the RCA sub connection to the sub setting the crossover point on the sub to best compliment your speakers and run speaker wires to your main speakers. With the RCA approach you would be running the main speakers full range. Using your sub the way you have been you are removing low bass frequency from the mains. I would try it both ways and see which approach best serves.

How low do your main speakers go down to? A sub is for 'sub' low bass that the main speaker can't achieve. If your main speaker has good lower ranger woofers I would let them do what they were designed for. They can add punch and dynamics that you will eliminate if you cross over too high. I run main speakers full range and set the sub crossover to 40hz.  Connection goes from amp high level output to speakers then to sub high level input. This way you pick up the same characteristic tonality and dynamics of the amp.

...I run main speakers full range and set the sub crossover to 40hz. Connection goes from amp high level output to speakers then to sub high level input. This way you pick up the same characteristic tonality and dynamics of the amp.

This is how my sub is set up also....the sub's low pass set at the lowest possible setting, and just enough gain to be barely audible on bass heavy passages.  I don't "feature" the sub.   Every room and situation is unique, so YMMV, but my main speakers go pretty low, and I just use to sub to help augment the output of the bottom octave or so in a large room. I also prefer not to run the mains through the sub’s high pass filter.

Your post omits a lot of relevant information.  The Yamaha Sub output frequency and slope is not specified in their spec sheet or in the manual, although some online say it is 100Hz, others say 90Hz.  [In the past (before digital bass management) Yamaha always had the sub out at 140Hz, 12dB/Oct].  You neglect to identify your subwoofer, except to say it has speaker wire in and out.  Some subs put an electrolytic cap in series with the speaker output affording 6dB/Oct. High Pass attenuation to the attached speakers, others don't (and whether an audiophile wants a cheap electrolytic in series is also a question).  You also don't say what your speakers are, and whether your system's subwoofer implementation up to now has been satisfactory to your taste.  Your new amp has no preamp in/out connections, so a real crossover cannot be used.  My advice is probably to continue using it as you have been, but filling in the missing details might make me revise that opinion.