Let's say that you've stored the row, column combinations that need replacing in an array called rc. Then just do
numberOfElements = size(rc, 1);
for k = 1 : numberOfElements
row = rc(k, 1);
column = rc(k, 2);
str = sprintf('Enter the value to go into row %d, column %d', row, column);
a(i,j) = input(str);
This will ask for only the table elements that you've specified in advance rather than all of them. For a little nicer program you should use inputdlg() instead of input().