Can this be clarified please:

1. Suica Nex at Narita: are 2 tickets issued: 1 for the Nex ride,(?same as the reserved seat ticket you are given when using a JR Pass from Narita) and a Suica "electronic" card

2. 3500Y cost: 2000Y for NEx, 1500 Suica

Yes, you get a ticket for the NEX ride and a Suica card with a balance of 1500 yen. When passing the gate at Narita Airport, use the NEX ticket, not the Suica card.

3500Y cost: 2000Y for NEx, 1500 Suica

The package costs 3500 yen and includes a Suica card with a balance of 1500 yen and a refundable deposit of the Suica card of 500 yen. So, effectively, the NEX ride costs you 1500 yen.

500Y deposit: this is my biggest confusion:
1500Y Suica means 1500Y worth of rides, or 1000Y worth?

The card will have a balance of 1500 yen to be used. The 500 yen deposit is separate.

What happens when you have less on the card than the ride you have just taken

Then you can use a "fare adjustment machine".

Can you recharge this Suica card: if so, how?

After which you go to the fare adjustment machine and pay the difference.

Yes. For the Suica part, you pay 2,000 yen, 500 yen of which is used as a deposit, and you get a Suica Card with 1,500 yen e-money.

Once you enter Suica (& PASMO) network with a Card, you have to use the same card to exit the network.
I recommend holding only one Card and keeping its e-money at least at 150 yen while you are outside the network.
When the e-money of the Card falls short of the minimum fare (i.e. when the amount of the e-money can not afford a ride to any other station in the network), you can not even enter the network with that Card.

: 1. Suica Nex at Narita: are 2 tickets issued: 1 for the Nex ride,(?same as the reserved seat ticket you are given when using a JR Pass from Narita) and a Suica "electronic" card

A N'EX ticket in a Suica & N'EX package has two roles.
This ticket works as a Ltd. Express ticket to take a Narita Express [N'EX] train, and also as a one-day fare ticket valid within a designated area (showed in yellow on this map) around Tokyo.
http://www.jreast.co.jp/e/suica-nex/guide.html
Unless you go on the same section twice or more in your route, you can get off a N'EX train at Station A (e.g. Shinagawa), take another train, and exit JR-East by passing through a gate at Station B (e.g. Ueno), all in the same day.

You are not given a ticket with these two roles when you buy a ticket as a JR Pass holder or just buy regular tickets.

Thanks.

This N'EX ticket works NOT as a one-day Pass, but as a one-day fare ticket valid only until you get out through a gate of a station.
This N'EX ticket may help when there is no N'EX train stop near your first destination.
If you plan well for your first day, you can travel with this N'EX ticket to a station which is a bit far from your hotel, then travel with a Suica Card gradually approaching to a station which is close to your hotel.
They don't cover charges, but I think you can complete your one-day trip in urban Tokyo on fare-only trains such as JR-East Local / Rapid trains, Keisei Local / Ltd. Express trains, and subway trains on Tokyo Metro or Toei subway lines.

Have a nice trip!

The bottom line is:

You are NOT going to rack up a huge cost on ANY local public transport in Japan, so you really DON'T need to worry about saving a few hundred yen, and spend hours trying to figure out the best cards to use.

Get a PASMO or Suica, enjoy using it, if the money runs out, top up more.

SUICA which is is the main thread is about isn't a pass.

It is a prepaid card and money is deducted each time you use it, there is no discount.

The special NEX narita express ticket is only 1500 yen vs 3500+ for a full priced ticket.

Can I confirm if this Y3500 card can be used for travel on NEX from Narita to Yokohama?

As well as train service within Yokohama?

It is not a card, but a package consisting of a NEX ticket and a Suica card.

The NEX ticket can be used all the way from Narita Airport to Yokohama (or even as far as Ofuna on Ofuna bound trains).