Not recommended travel multicities. Vacation should be hassle free

aren't this depends on your preference? its doable. that's why they do sell JR pass that covers from tokyo to hokkaido

Quite obvious isnt it, if your question is not about hassle free or not.
You have already make plans on your travel, so whats the point of going back to Chitose to fly back. So what do you really want to know?

Do day trip from Tokyo to Yokohama and take that Shinkansen lo.

Assuming that you have fix your trip to both Hokkaido and Tokyo, I guess your plan is pretty much good. Cause you still need to get to Tokyo and the other way is to fly from Sapporo. As others have suggessted, take a short trip around Tokyo area. You can even take a trip to Karuizawa using the Tokyo WIde pass which is about 2 hours journey and spend a day there.

Too much at Otaru
Btw, you no need to overnight at Otaru, Just depart from Sapporo morning and back to Sapporo at Night. 1 full day at Otaru enough cover it all.
Even Furano at April no lavender, but those Hokkaido sweet corn & fruit still worth to visit at Tomita Farm

Otaru more like craft town and alot more on dessert and bakery
Asahikawa more like hunter, more towards meat side. (Santouka Ramen born place)
Hakkodate more on western because early age open port to west.
Sapporo got overall of all food. It still got biggest fish market at Hokkaido.

If you want eat best Corn ever taste in your life, it worth to visit Tomita. It also got 2nd best melon too. 

Best Melon in World still at Xinjiang, China

Nippon rent a car and Toyota rent a car
This 2 are my usual one. Very reliable.

Since going as family size, car renting are more bettter option plus april, no icing road.

So my suspicion was correct, you ARE trying to cheat the hotel. For this sort of hotel that clearly charges extra for 2pax in the same room, if both of you turn up at the front desk you will likely be charged for your 2nd guest.

If you insist on going along with this penipu scammer arrangement anyway, then during check in / check out, you go to the front desk alone and ask your wife hide somewhere else in the lobby or outside the hotel first lo.

Note that many business hotels have really small lobby areas and the guest lifts may even be in full view of the front desk.

Nippon rent a car and Toyota rent a car
This 2 are my usual one. Very reliable.

Since going as family size, car renting are more bettter option plus april, no icing road.

We travel around with my boy since he was 3yrs old. Every online booking, we will indicate 2 adults n 1 child (provide age info). We don't really bother if they charge for the kid or not, just to make sure stress free for a vacation. And if any argument on hotel arrangement, with a booking properly said number of pax will always win. Recent trip, we booked a suite room in a osaka hostel. Booking indicated 2 single bed + 1 sofa bed for us 2 adults + 11yr old child. When we were there, the reception behave as in not expecting 3pax. When I insist we booked for 3pax and it mentioned sofa bed, she insist they only have sofa in the room, not sofa bed. Anyway, I don't care, and tell her my boy can have the sofa...or whatever, we just want our room without extra charge as my booking is accurate, hotel info misleading. In the end, they setup the sofa bed for us. Guess what, it really is sofa bed in the room. But don't know why they try to be funny with us.

For Japan, it is better to get a bed space for each pax. Unless you go for premium hotel or you all really small built. As you don't really know if their bed big enough to share.