As with weapons and most other items, you can examine a parasite before you acquire and equip it. Your display will list the positive and the negative effect, eliminating any guesswork. You can also mix and match as many as six parasites.
Some parasites and artifacts may have an effect that counteracts a negative effect put in place by parasite you have already equipped. For instance, you may find a parasite that slows your weapon’s alt-fire charge rate. That is a negative effect, but another parasite or artifact might improve your damage dealt while your alt-fire shot is recharging, which turns the effect into a net positive.
Pay close attention to artifacts and parasites you come across for this reason, and remember that sometimes the right choice is to leave a parasite where you find it. You don’t necessarily want to equip a parasite that produces a positive effect if it also damages you whenever you open a chest, for instance.
Though parasites may appear just about anywhere, keep in mind that they are especially likely to appear in bonus rooms (accessed by finding a point of yellow energy on a pedestal or in an alcove that doesn’t appear on the map). If you drop into a room full of purple acid bubbles, break them all apart with your sword and often you will reveal a parasite or two.