In some states, you can countersue as long as your claim arises out of the same event or transaction. In fact, in some states you must file a countersue if you have a claim against the other party; in those states you cannot sue over the same dispute in a later lawsuit.
If the amount you sue for is under the small claims limit, your case will probably remain in that court. If, however, you want to sue for more, check with your small claims clerk for applicable rules. Often, you'll need to have the case transferred to a different court that has the power to handle cases in which more money is at stake.