Specifying a Diff-In-Diff with multiple treated groups over multiple years
Firstly, the diff-in-diff already is a fixed effects estimation. If you run a regression with FE and your time variant terms ($S_i*T_t$ and $T_t$) as in the plain and simple diff-in-diff setup, as such:

$$ Y_{it}=B_0+B_1T_t+B_2S_i+B_3S_i*T_t+e_{it} (1)$$ 

You should obtain similar results. Secondly, your specification -- since it will be on a multiple treatment setup -- should consider if your treated groups in different periods of time are disjoint, that is, if a unit of observation might receive the treatment multiple times. Considering that adding a fixed effects in time might be convenient for your estimation, as you were considering, I would work with the following specification if the the treated groups are disjoint:

$$ Y_{it}=\alpha_0+\alpha_1S_i*T_t+\alpha_2S2_i*T2_t+v_t+u_i+e_{it} (2)$$ 

And if they are not disjoint, I would consider a interaction between the treatment effects:

$$ Y_{it}=\beta_0+\beta_1S_i*T_t+\beta_2S2_i*T2_t+\beta_3(S_i*T_t)*(S2_i*T2_t)+v_t+u_i+e_{it} (3)$$

You should also consider testing the common trend hypothesis, since you still need an adequate control group.