You could just read in the existing worksheet and find out the last row:
if isfile(filename)
% Read in existing file to get its last row.
[numbers, strings, raw] = xlsread(filename);
[rows, columns] = size(raw);
else
% File doesn't exist yet.
rows = 0;
columns = 0;
end
then when you make up a cell reference, start writing at the next row
nextRow = rows + 1; % Or wherever you want.
cellRef = sprintf('A%d', nextRow);
xlswrite(filename, data, worksheetName, cellRef);
