So that's several subproblems to work on (and working on subproblems is good, since you can solve one subproblem without worrying about the others at all):
1) Getting input
2) Deciding, given a string, what to do about it (is it an assignment, or a formula, or what)
3) Given a cell reference, how to determine what cell it refers to
4) How to store a formula in your array
Using a two-dimensional array is dead simple: you give the row index and the column index and you're done.
two_d_array = 4; //set the element in the sixth row and ninth column to 4