I would not use the "Answer" box if your reply is not really an answer. The creators of this site see the comment feature as a privilege, and you need to show a little experience with the system (via your reputation) before you get it. The focus is on the questions and the answers, and this is a easy way to keep spam lower.
If you have a possible answer to the question, but only in some constraints, state it that way in your answer: "If this-and-this is the case, you can do that-and-that." That would be a valid answer, and I think you can use the comments on that answer.
If you have a related question, you should create a new question, and refer to the first question via a link. Asking a secondary question via comments is never a good idea, since they don't have the same visibility as a real question.
The best thing to do is participate more, and you'll get that 50 rep in no time. If you want to understand why your rep is so low, you can watch the graph, or even better, the audit.