Questions about transportation

Hi there,
Me and my wife will travel in Japan for 2 weeks and a couple of days. I would like to know what pays up the most regarding what kind of passes should we buy.
This will be our itinerary arriving at Narita airp.
- 5 nights Tokyo
- 1 night Nikko
- 1 night Shirakawa-go
- 2 nights kamikochi
- 2 nights Takayama
- 4 nights Kyoto
- 1 night Tokyo to take the flight home from narita

We are thinking on buying a 2 week JR pass and use it for the last 14 days, and also a SUICA card so we can move around Tokyo and Kyoto. Can someone give some pointers and advises.
How does SUICA works, should you buy it and load it each day you want to use it? How much does it cost?

Thanks

If you order the sights in a meaningful order, then a Japan Rail Pass will not pay off, and it will be cheapest to use regular tickets:

Tokyo (with side trip to Nikko) - Kamikochi - Takayama - Shirakawago - Kyoto - Tokyo

Indeed, it is a good idea to also use Suica. It is explained here:
http://www.japan-guide.com/e/e2359_003.html

Thanks for the comments, I've actually tried to compare with the prices given at Hypedia and it as about the same as the cost of a JR pass. I've seen that there is a somewhat big difference if you reserve a seat or not, but if you travel with a Jr pass is it that you don't have that option?

Regarding the SUICA IC card, you can use for the Tokyo Metro but can you use on other type of urban semi-urban railways around Tokyo, like the Yamanote Line for example.
Can I use the Suica from Tokyo main areas to travel to Takaosan or to Hakone or even Mt. Fuji?

The JR Pass allows you to make free seat reservations. You can choose to travel in a reserved or unreserved seat, but you must make reservations for the reserved section.

The problem you're going to have is that, while you may calculate all your trips and the cost may be comparable to the JR Pass, you'll need to make all those trips with the 7 consecutive calendar days for which the pass is good. One cannot pick and choose which days you'd like to use the pass. Once you tell the attendant which date you wish to start the pass and he/she stamps it, you have 7 (or 14 or 21) days to use it.

Thanks for the comments, I've actually tried to compare with the prices given at Hypedia and it as about the same as the cost of a JR pass.

Then you are doing something wrong.

Here are the costs:
Tokyo-Nikko side trip: about 3000 yen
Tokyo-Kamikochi: about 7000 yen (JR as far as Matsumoto)
Shirakawago-Kyoto: about 7000 yen (JR from Kanazawa)
Kyoto-Tokyo: about 14,000 yen

Grand total: 31,000 yen

Cost of a 14-day rail pass: 46,390 yen

I don't see how you get close to it even if you include some urban JR rides and airport access.

I've seen that there is a somewhat big difference if you reserve a seat or not

No, the difference is typically around 520 yen between reserved and unreserved.

Regarding the SUICA IC card, you can use for the Tokyo Metro but can you use on other type of urban semi-urban railways around Tokyo, like the Yamanote Line for example.

Yes, it covers virtually all trains and buses in Greater Tokyo.

Can I use the Suica from Tokyo main areas to travel to Takaosan or to Hakone or even Mt. Fuji?

Takaosan: Yes
Hakone: Yes
Mount Fuji: No