@Chris1983 Stop panicking and over thinking the project chap, the supply to your SCR, Amber Valley or not, comes from the alternator and goes onwards to the leisure battery, if it has a trigger wire on it to operate the SCR then that may well be used by your new B2B unless that's a voltage sensing type but your new B2B charger should be able to sit where the old SCR did.
Whip the seat out and start setting spaces out for your new layout but again don't panic, with a 100Ah lithium LB you're going to have shed loads of space, I've got nothing under the double passenger seat as that's where the shoes and wash bags go.