What I did to install Coq 8.8.1 with equations 1.1 as a separate profile:
opam switch coq-8.8.1 --alias-of 4.06.1
eval `opam config env`
opam pin add coq 8.8.1
opam pin add coq-equations 1.1+8.8
opam install ott coq-ott
(opam pin -y add coq-equations 1.1+8.8 && opam install -y ott coq-ott)
I lack notes, but you can repeat opam switch profileName --alias-of 4.06.1
more times