First, I'm not familiar with the Pacific routes. But here's what I can tell you.
BEBOP is the first navigational intersection, a fix. It is the name of a point in space defined by lat/long or by a radial from a VOR (land based navigation radio).
R464 is an airway. Think highway in the sky. Since it is over the ocean, it is probably defined by drawing a line through multiple lat/long points. The plane will fly it using some combination of GPS, INS, or IRS. INS and IRS is a type of position sensor used on planes. It uses gyros to determine acceleration/deceleration in all axis. If the plane knows where it is at the start, then it can use acceleration data to figure out where it is throughout the flight.
BANDY is another intersection. Although I don't know why it is listed since it is on the R464 airway.
MAGGI is another intersection. In this case it is probably the start of the arrival into Hawaii.
MAGGI3 is the name of the arrival procedure into the airport. The arrival can be 200 to 300 miles long. It may contain multiple fixes to define the route along with several "step down" altitudes to keep the traffic flowing into the terminal area.
So the clearance BEBOP R464 BANDY R464 MAGGI MAGGI3 tells the pilots to program the Flight Management System (FMS) in that order. Leave the airport, SFO in this case, fly directly to BEBOP, join the R464 airway to BANDY, continue along R464 to MAGGI, and then fly the MAGGI3 arrival into Honolulu.
Piece of cake.
