I'm not exactly sure what you're trying to say. If by "seeing" you mean "dating" the phrase would be, "I haven't been seeing him for long." If you mean you haven't seen him in a long time the phrase would be, "I haven't seen him in a long time." I hope that helps....

**I haven't been seeing him long.** to be seeing someone = to be dating someone

I agree, it sounds like you're asking about how long you've been dating. By themselves, "I've not seen him for long" means you physically saw him for a short time (like he was passing by?). "I've not been seeing for long" sounds strange, it sounds like you've recently had surgery to cure blindness and visual things are new to you. If you don't say what you are seeing, then the meaning of "to see" reverts to your own ability to see or to understand.