I'll give my (There are different alternatives) answers below to some of your questions: I fly the 777-*** variants all the time so not much difference to 787
Flightplans, I use
http://onlineflightplanner.org/ for my flightplanning, enter all the info' untick the ".pin and .pdf" settings and tick .fgfp setting then "create plan" save this plan to a file on your desktop named say flightgear flightplans. When you want to use this click on the "autopilot" tab, Open the "route manager" tab, in the route manager box click on the "load" button and then find the file on your desktop click on it. It will then load the list of plans within the file click on the one you wast to use, it will bring up the plan in the route manager box. Use the RWY box to state your departure RWY, click on SID box to set "default" SID. Click on the RWY box at your destination airport enter the RWY you intend to use and set "default" approach in the box. all done Click on the "activate" box now this route is set into the autopilot. You can set in altitudes of climb within the waypoints if you want, but I won't go into that now. If using a ILS approach don't forget to set your radio (F12) to the correct settings for the radial and frequency or your plane will not pick up the ILS!!! When you start at your departure airport click on the LNAV button to turn it on, your plane will now follow the flightplan when you click the autopilot button after you have taken off. ( The autopilot WILL not work until you are in the air above 400ft) Don't forget also to enable your auto throttles once above 400ft click the AT button and the autopilot will follow speed set in the route manager box.
Be patient though it took me six months to learn the 777 (and I'm still learning today) I have over 1800 hours flying the 777. Hope this answers the question about flightplans?