From the documentation (type doc xlswrite):
xlswrite(filename,A,xlRange) writes to the rectangular region specified by xlRange in the first worksheet of the workbook. Use Excel range syntax, such as 'A1:C3'.
You can use some counters to keep track of what the first empty row is, or use xlsread to find that out. (note that xlsread will generally not output empty rows and cols, that behavior is not well-documented)