I've been using this from the outset- it's a great product, especially if you're in an area with annoyingly old pipes. But, there are some tricks to using it especially if you're trying to cycle a tank. Firstly, only treat the water that is going into the tank, never the entire thing unless you've had a massive ammonia spike and your aquatic family members are at risk. If you can get a 0.01mL graded syringe, you can measure it out quite accurately.
Secondly, if you can let it sit for a bit (the longer the better), do so. Not only will the Prime have a better chance to knock out all the nasties, but your water will age slightly and the chances of it impacting the rest of the tank will be drastically reduced.
Finally, like any product- be responsible in how you're using it. Don't overdose it unless you're in a situation where it is 100% bonafide required (deshelling baby brine shrimp, for example is where it comes into its own), and if it ever (like it's going to happen....) gets to the point where it expires, chuck it.
Hope this gives you a better idea of how to deal with it