Oh, thats what you mean. You are right, some herbs are difficult to distinguish.
Both Deathweed and Waterleaf have specific blooming conditions. Deathweed blooms only during a Blood Moon, and, as far as i know, since 1.3, also during a full moon. When it is blooming it emits a faint glow, so it's best to plant it in a dark area.
Waterleaf blooms only when it is raining. I think it does not glow, but with a bright background, blooming Waterleaf is easy to see.
Unkalibriert's tip of using a Staff of Regrowth is great, that item is now usefull since 1.3 :) Also it's a lot easier to find. Look for giant trees in the underground Jungle, similar to the giant trees on the Surface. If they are hollow, they will have a chest at the bottom, with a very high chance for a Staff.
If you use the Staff to harvest, it will only destroy blooming herbs, and you will even get more seeds and herbs, than ordinary harvesting with a pickaxe. That, and the addition of the new alchemy table, water bottles stacking to 999 and the new planter boxes sold by the dryad, makes alchemy much more viable now.