Purchasing tickets for specific destinations

Hi,

Am I supposed to buy a ticket for specific destinations in advance? For example, if I want to travel from Tokyo to Kyoto on a specific date at a specific time, can I book that ticket in advance? Is there assigned seating on the trains?

It sounds like with the JR Pass I get an exchange order which I need to take to a kiosk in the country and exchange it for an actual train pass there. If that's the case than can I put a hold on a specific train in advance? Maybe the trains aren't that crowded and you don't need to but just looking for some advice.

Thanks!