On the JR-Central website, you can see the images of JR basic-fare ticket and Shinkansen reserved seat ticket.
- JR-Central: How to read the information on the tickets https://global.jr-central.co.jp/en/tickets/read/
You put the both tickets together in a ticket gate machine
when you enter the Shinkansen at Shinagawa
and when you exit the Shinkansen at Gifu.
To take a Shinkansen train,
you pay for the Shinkansen surcharge and buy your Shinkansen super-express ticket,
for your train ride either with your seat reserved or without seat reservation.
After getting off your Shinkansen train at Nagoya,
you follow signs for JR lines and reach Shinkansen North or South transfer gate.
(The signboard above the transfer gate says "Transfer to JR Lines";
you don't find the term "transfer gate" but please don't feel getting lost.)
Regarding Nagoya -- Gifu leg,
as Uji mentions, you don't have to choose a Limited Express train;
you can take any Gifu-bound Local train or any Ōgaki-bound or Maibara-bound rapid train.
To take a JR Limited Express train,
you pay for the Limited Express surcharge and buy your Limited-Express ticket.
For JR conventional lines, in most cases, ticket gate machines would not check Limited-Express tickets.
I recommend that you apply for the three JR tickets together in advance,
in which case your get a 50 percent discount for the Limited Express surcharge,
on the condition that you make the transfer in one same day.