You could try selecting the land using Select>>Altitude Range from a low of 0 to a high of 10000000. Then your edits will only affect the previous land area.

There isn't a way I know to set a lower altitude cap on tool effects. If you're getting deep pools with the prescale offset tool, though, you likely have the value set too high (I generally use something on the order of 0.01 or less for prescale tools).