That's pretty much up to you. Level adjustment and racial hit dice are both I think pretty authentic to PNP, but they aren't turned on by default. Instead, you can turn them in with the appropriate switches. (The PRC radial menu has an "alter code switches" choice that lets you access these options.)
I have never been a fan of racial hit dice, mostly because it limits build possibilities in a way it wouldn't in PNP. I would probably turn level adjustment on in an average difficulty module. If you are playing a really tough module, you can probably leave LA off and still not have a problem with making the module too easy.
