If you don't mind I'll use this thread to list the steps needed for joining a mkv. I'll just cover the first movie since you must trim both discs.
1. Create both mkvs using whatever programs you prefer.
2. Open FOTR part 1 in mkvmerge.
3. Set the output filename to what you want.
4. Note the number of chapters (27).
5. On the global tab, check Enable splitting... ...after this duration. Place 6338s in the box.
6. Start muxing.
7. When complete, close mkvmerge and open FOTR part 2 in mkvmerge. I tend to close it between uses so I don't miss a setting I needed to clear from the last step.
8. Set the output filename to what you want.
9. On the global tabe, check Enable splitting... ...after this duration. Place 00:00:00.500 in the box.
10. In the max. number of files box place 2. This is important as without it you will end up with a lot of files 1/2 a second long.
11. Start muxing.
12. When complete close mkvmerge and open it again.
13. Go to the Chapter Editor tab and drag the FOTR part 2 mkv into the chapters box.
14. Select each chapter in order, changing the name to the next number after the number of chapters in FOTR part 1. Chapter 1 becomes Chapter 28, Chapter 2 becomes Chapter 29, etc.
15. Once finished, on the menu click Chapter Editor > Save.
16. Close mkvmerge and open FOTR part 1 in mkvmerge.
17. Click append and add FOTR part 2.
18. Set the output filename to what you want.
19. Start muxing.
FOTR EE Part 1 end = 6338 seconds
TTT EE Part 1 end = 6396 seconds
ROTK EE Part 1 end = 7656 seconds