You can set the initial spin on each atom in the .cell input file. All you have to do is to find the entry for the atom you want in the atomic positions block (either positions_frac or positions_abs) and then add to that line the text: "spin=" followed by the spin you want, either positive or negative, in units of hbar.
For example, to set a collinear spin of -2.2 on an Fe atom at fractional coordinate 1/4 1/2 1/4 you would edit the positions line to say:
Fe 1/4 1/2 1/4 spin=-2.2
You can set the initial spins of any (even all) atoms in the simulation cell like this.