The presence or absence of "again" is totally unrelated to the difference between "sorry for + gerund" and "sorry to + infinitive." All four of the following are possible and perfectly natural:
- Sorry for bothering you.
- Sorry for bothering you again.
- Sorry to bother you.
- Sorry to bother you again.
"Again" is simple: you can include this if you have previously "bothered" this person and are apologizing for a second or subsequent occurrence.
The difference between "sorry for" and "sorry to" is more subtle. "Sorry for bothering you" works when you have already bothered the person -- not necessarily a second occurrence, but the bothering has already begun, so to speak. It would fit at the end of the conversation. The thing you are apologizing for is a concrete thing that has already happened or at least started to happen.
"Sorry to bother you" works better at the beginning of the conversation: the thing you are apologizing for is a detached, almost hypothetical thing, as if it hasn't occurred yet or is only just starting to occur.
The distinction between the two is a little blurry, and if you said "sorry to bother you" at the end of the conversation -- or "sorry for bothering you" at the beginning -- it's unlikely anyone would even notice, let alone care that you used the "wrong" form. So don't worry about this too much, but here's a simple scenario to help it stick in your mind.
- Sorry to bother you -- could I borrow your pencil?
- Sure. Here.
- Thanks. Sorry for bothering you.
- Sorry to bother you again -- could I borrow your eraser?
- Sure. Here.
- Thanks. Sorry for bothering you again.