How should I install Far Manager into Cmder?

Actually, doesn't matter where you've installed Far Manager. The only significant condition - Far must load ConEmu plugin.

1. Update ConEmu to the latest build.
2. Install Far using msi package, goto ConEmu settings and press "Add default tasks" on the tasks page. Far task will be created for you.
3. Or, you may create task manually - just don't forget about /p switch - pass both ConEmu/plugins and Far/plugins folder.

Also. You can unpack Far distro into "conemu-maximus5" folder (far.exe will be in the same folder as ConEmu.exe). In that case you may just run "far.exe" from new console dialog.