I recommend you check out Google Maps, but be warned: Google isn’t always 100% accurate. Also, for your time in Tokyo, I recommend you check out the Tokyo Metro website. Download their app and the English route map (pdf). The Tokyo Metro App gives you point to point pricing between stations on both the Tokyo Metro and Toei lines. In the Android store it’s called “Tokyo Subway Navigation” and can be used off line. I would use Google Maps to find out where the nearest station was to me and my destinations and to get a rough idea as to what the possible routes are.
If it was me, I’d get the one week JR National pass no matter what. The pass costs about the same as a round trip on the Shinkansen (bullet train) between Tokyo and Osaka and will also cover the ride between Osaka and Kyoto, so it’s a no brainer. How you use it (when you enable it) will depend on what your travel plans are around your Osaka/Kyoto travel. If you activate it wisely, you might be able to spend less on Metro passes. Regarding the Rail pass, you’ll need to exchange your voucher for your actual pass prior to using it. The pass is based on calendar days so if you were to activate it at 23:59, that last minute of the day would count as 1 day and you’d have only 6 left after that, so activate wisely. Google “Exchange JR Pass Vouchers” for exchange office locations and times of operation. Also on that page is a link showing maps of some of the exchange offices.
The Shinkansen travels from Tokyo, through Kyoto, then to Osaka, so you want to either hit Kyoto on the way out or the way back from Osaka. One way ticket on the Shinkansen from Tokyo to Osaka is around $150, so round trip would run you about $300. 7 day National (not regional) JR Pass would run you around $280, so price wise, they are close. If it was me, I’d get the JR Pass as it includes the Shinkansen AND gets you access to local transit like the Tokyo monorail, Yamanote line and other local JR resources (buses, ferries, etc…). The Monorail runs between Haneda Airport and Hamamatsuchou. There are local, rapid and express lines. Local stops at every stop, rapid at a few and Express which only stops at the various airport terminals and Hamamatsuchou. The Yamanote line is basically a ring that hits a lot of major metropolitan areas in Tokyo. There are a lot of rail companies in Japan. JR is the largest. Even with that, there are many subways, trams, trolleys, etc… which are NOT JR affiliates so even with a JR pass, you may find it necessary to purchase additional passes, take a taxi or be prepared to walk a fair distance.
Regarding the Suica card, my understanding is, it is basically a pre-charged card that is drawn from each time you swipe it. I don’t believe there is any discount from paying individually, it’s more of a convenience thing. Without the Suica card, you’ll have to purchase a ticket at each entry gate. The nice thing about Suica is that it is accepted pretty much universally in the metropolitan Tokyo area. So is cash (at the ticket machines). 
Aside from the convenience, I don’t see much benefit.
We were in Japan in October of 2017 for 2 weeks and got the 2 week Green Car pass. We would have been fine with the regular pass, however we were travelling with a larger group of older people who wanted the added comfort. In any case, while in Tokyo, we tried to use our JR pass as much as possible, but it wasn’t always possible. Many of our trips required lines on the Tokyo Metro and/or the Toei lines so on days which we made a lot of trips, we bought the Common one day ticket for 900Y. In retrospect, that wasn’t the best choice. For travel in Tokyo, you might consider the Tokyo Subway Ticket. Tokyo Metro has 24, 48 and 72 hour passes (800, 1200 and 1500Y) for visitors (you need to show your passport). The passes grant users unlimited use of the Tokyo Metro and Toei lines for 24, 48 or 72 hr from the first time used. Obviously, you have no need to pay for a Tokyo Subway pass while you’re in Osaka/Kyoto, so plan accordingly.
Here’s the link to the Tokyo Metro subway pass info. Also has locations where you can purchase, etc…
If you want to save money, you have to put in some time and plan. On days where you are not travelling far or often, it might be cheaper to paint point to point. Minimum price (between adjacent stations) is 180Y. Not knowing what your plans are, I can’t tell you what would be best. Not being married to you, I have no incentive to try. 
Oh, being from Chicago, I’m sure you are familiar with what it’s like to use public transportation during rush hour. Japan takes that to a whole other level. I’m sure you’ll be fine, but the wife and I chose to either wake up REAL early and avoid traffic OR have a relaxed breakfast and wait for it to subside,
Sorry, I had more links, but I’m limited to 2 as a new member.
Enjoy your trip!
