There are a number of ways you can do it. It all depends on how you want it stored. personally I would store them in a 2d array instead of 1d. so it would be like
char array[5][45];
so char [0][x] would hold the data from file 1 char[1][x] would hold for file 2 and so on. It shouldn't be too hard for you to do and you can have it assign to the proper part of the array when its reading in so you wont have to break it up after.
Maybe indicate the end of each section with the null-terminating character? For example, the first X bytes are for 1 file. The next byte is a null-character which indicates the end-of-section. After that, another X byte section for another file.