God created male and female.... What about those who do not fit in the box? Often times I hear the argument that marriage is between a man and a woman, God made them male and female, (adam and eve not adam and steve ..etc).
My question is for those who do not fit into the gender boxes we like people to fit into.
In fact there are many variations of gender between the poles xmale, heterosexual, masculine 
and xfemale, heterosexual, feminine.

For the sake of specificness we will drop the heterosexual part and look a little closer at just the gender aspect. 

What happens when a physical check shows one sex/gender and a chromosome test shows another?
"it would seem a simple case of checking for XX vs. XY chromosomes to determine whether an athlete is a woman or a man, it is not that simple. Fetuses start out as female, and the Y chromosome turns on a variety of hormones that differentiate the baby as a male. Sometimes this does not occur, and XX people with two X chromosomes can develop hormonally as a male, and XY people with an X and a Y can develop hormonally as a female."
http://www.nytimes.com/2009/08/22/sports/22runner.html?em

Stories like Santhi Soundaragjan, who after gender testing failed as a female and was stripped of her Olympic medal. Her condition was possibly "Androgen Insensitivity Syndrome (AIS). This condition includes the existence of a 'Y' chromosome in phenotypic females (typically only associated with a male genotype) and results in an inability to respond to Androgens. This unresponsiveness leads to a female body without female internal sex organs. Although the body produces testosterone, it does not react to the hormone." from http://www.taipeitimes.com/News/sport/archives/2009/06/11/2003445882 (The failed test even led to a suicide attempt) 

There is more...amidst the many varying conditions that fall somewhere inbetween, there are those who are born with both genders, the hermaphrodite. 

Where do these people fit into normal Christian male/female scenarios? Do they have room for them?
As with many of these questions, some of the answer is already in the question. You've termed occurrences like this "conditions" - in other words, deviations from the general norm. As with other medical conditions they are a result of The Fall. So the line you quote is correct, God created male and female, very clearly and distinctly.

So, how do people affected by these conditions fit into the "normal Christian scenarios" of male and female? Well firstly there's nothing explicitly Christian about recognising that the norm is to be male or female. Secondly, as we both have already pointed out, these are medical conditions, so I would suggest they warrant expert medical attention. Thirdly my understanding is that in most cases there is a "leaning" towards one gender or the other that can help to establish which gender a person really is.

Finally, your last question, "do they [Christians] have room for them [people with these type of conditions]?" Of course. Anyone and everyone has the potential to become a Christian and should be welcome in Church. There should be a note of caution taken here though. Many people, inside and outside the church, find these issues very confusing and may struggle to react in the way they perhaps should. Some may be overly curious, others may find such a condition distasteful and not want to confront it. Nobody is unwelcome but not everyone will necessarily be able to express that. And that's ok, the church is made up of all kinds of people, not all of whom will see eye to eye all the time.