I guess i worded myself wrong. sorry about that.
After the positive effects are over do I have to wait until the negative effects are over to effectively use the drug again? I noticed that after I used a cig my PE went down a point so i took another cig and it did nothing.
Let me paraphrase what RavenousRat has already said.
If you want another dose of a given drug to work, you have to wait until the effects of its previous dose have worn off, both positive and negative.
This should not be confused with the effects of addiction, which can be 'cured' by taking another dose of a drug to which you are addicted, and only appear after that drug passes through your system.
Let me illustrate that using buffout as an example.
You take a dose of buffout, which gives you +2 bonus to strength and endurance, but reduces your agility by 1. If you take another dose before your strength, endurance, and agility are back to normal, you will see no effect whatsoever.
However, if you get addicted, the addiction to buffout will reduce your action points by one. That has nothing to do with the drug itself, it's just how addictions work here. That effect will appear as soon as the drug is out of your system, and can be 'cured' by taking another dose, after which your strength and endurance will receive a boost again, your agility will get reduced by 1 again, and the addiction penalty will no longer affect you as long as the drug lasts. Of course, you can also simply wait for the addiction period to end (unless you're addicted to jet, in which case there's no way to recover from the addiction).
I hope that answers your question.
By the way, if you're looking to buy any drugs, PM me.