Exactly. It pretty much depends on the pest you are trying to kill. I start with a general dip in Coral Rx first (used to use Lugol's, but it was just too harsh sometimes). If I find anything, I'll treat further. For example, if I buy a coral, I'll break the base off (to prevent nuisance algae & montipora eating nudibranch eggs), dip it in Coral Rx per the instructions, and if I find flatworms, I'll dip it again in something like Salifert's Flatworm Exit just to be extra safe. Or, if I find red bugs, I'll use Interceptor. Etc.
But yes, just use the water from the LFS in a container, add the dip solution per the instructions (or instructions found online like in the case of treating zoanthids with Furan 2). You can treat more specifically a second time if you find something.
I still recommend quarantine after dips though. You never know what you'll miss in a dip until it's too late.