You can eliminate the problem altogether by shortening your sentence:
I didn't understand a friendship between a guy and a girl, but now I do.
Another way to say it:
I didn't understand a friendship between a guy and a girl, but now I understand.
Or, informally:
I didn't understand a friendship between a guy and a girl, but now I get it.
If you really want to specify what you now understand, try:
I didn't understand a friendship between a guy and a girl, but now I understand such relationships.
If you want to emphasize that it took you a long time to figure it out, use the tense in your first example, but try changing the adverb:
I didn't understand a friendship between a guy and a girl, but gradually I have come to understand such relationships.