There's no right or wrong way to do this. Distros like ClassicWB and BetterWB have become popular in recent years but I'm a fan of building up a system slowly by hand. Spend some time using your system and identify what your needs are. Then go to Aminet and browse/search for something that fulfills that need. Or borrow from one of the distributions.
For me, the essentials when setting up a new 3.1 system are
LhA,
DOpus, and
MUI. You'll probably want
WHDLoad, too.
