I'm going to assume that the issue is that you want to run this code again later (with different data), so you don't necessarily know, when you run it that second time, how much data is already in the xls file. In that case, a simple fix is to use exist to see if the xls file already exists. If so, use
[~,~,raw] = xlsread(file);
rowoffset = size(raw,1);
to work out how many rows to skip. (Set rowoffset = 0 is the file doesn't exist.)
Then use num2str to make the Excel cell references for writing. Eg
Cref = ['B',num2str(rowoffset+2)];
xlswrite(...,Cref);
