I have and have always had many close female friends. I don't see what's so special or "difficult" about these relationships, they function just like any friendship I have with a man or boy.
If you want to write about a male-female friendship, then just write a male-female friendship.
No, I don't constantly wonder whether or not I would like to have sex with my female friends. There are some, where that thought would never cross my mind, not because I find them unattractive, but because they are the kind of person that I don't feel sexual about. There are some that I would want as a sexual partner, but either they already have a partner or they don't feel that way about me, so that matter is settled for me and I no longer need to wonder. It's like deciding to spend the holiday in Italy instead of France: while in Italy, you don't constantly think about France, that would be dysfunctional. Instead you enjoy being where you are. So not lusting after someone you cannot have is simply the healthy way of being, and not difficult at all, unless you are the difficult kind of person.
Of course some of the things my female friends and me discuss pertain to our mutual genders, like asking for feedback on hair styles or getting a "male" or "female" perspective on a topic, but generally gender or sex don't enter into these friendships at all. We even sleep side-by-side chastely sometimes, and we hug a lot (like I do with my male friends).
If you write about a boy and a girl who are not romantically inclined towards each other, then write just that. It is not a relationship where a topic has to be avoided, but a relationship where a topic simply does not arise. Would you have to explain why two boys are friends instead of lovers? No. So why do you have to explain that about a boy and a girl?
Lauren suggested this edit to my answer: "Would you have to explain why two gay boys are friends instead of lovers? No. So why do you have to explain that about a straight boy and a straight girl?" (Italics are mine, to indicated the edits.) I rejected that suggestion, because I mean something different: When we read about two boys (or two girls) being friends, we expect them to have no sexual or romantic interest in each other, because that is how these relationships were portrayed for centuries and how the heterosexual majority of the population live their friendships. These kinds of friendships are the norm, and we see nothing strange or problematic in them. What we do find strange, abnormal and expect to cause problems are mixed gender friendships, because we cannot imagine them to be non-sexual. For some reason we feel that a boy and a girl must be about sex. But if you observe yourself, I am sure you will realize that you do not feel sexual about all people with the sex or gender you are oriented towards. Sex is not something that a heterosexual man must feel for all women (or a gay man for all men or a hetero woman for all men etc.). Sexuality is something that you feel for individuals, not for a category – or, if you want, the category is more complexly defined that by gender alone. So just because sex would be possible for a heterosexual by with a girl does not mean that it is possible for him with this specific individual.
As writers, we don't need to fall into the trap of thinking in categories. There is no such thing as "all men" or "all women" or "all English" or "all dark skinned persons" etc. People within these categories are as varied as between categories, so sex between one specific boy and one specific girl is as optional and likely as them having the same size of shoes or the same taste in music: they may or may not have it, and if they do have different shoe sizes or musical tastes you don't need to mention it in your story, unless your story is about that difference.