When considering a bilattice you need to distinguish two type of sites.
A B A B
-------o-------o---------------o-------o----
|<--a-->|<------b------>|
For instance you can denote the two kind of sites with letters $A$ and $B$ as it is shown above. Then you have now two different creation and destruction operators . $c_{iA}^{\dagger}$ and $c_{iA}$ in order to create or annihilate a particle in $A$ sites and $c_{iB}^{\dagger}$ and $c_{iB}$ for $B$ sites.
You have to be careful with indices $i$. With a simple lattice the sites had indices like that:
A A A A A
-------o-------o-------o-------o-------o
i-1 i i+1 i+2 i+3
|<--a-->|<--a-->|<--a-->|
But know the indices are different since there is two kinds of sites:
A B A B
-------o-------o---------------o-------o----
i i i+1 i+1
|<--a-->|<------b------>|
All this changes expressions of Fourier transforms and hamiltonian:
$$
c_{kA}=\frac{1}{\sqrt{V/2}}\sum_{i}{c_{iA} e^{i k r_{i}}} \quad \text{where} \quad
r_i=i*(a+b)
$$
$$
c_{kB}=\frac{1}{\sqrt{V/2}}\sum_{i}{c_{iB} e^{i k r_{i}}} \quad \text{where} \quad
r_i=i*(a+b)+a
$$
EDIT:The volume of the system has to be divided by two in Fourier transforms since there is now two sites in each primitive cell (there were only one before). END EDIT
The hamiltonian now takes the form:
$$
H=-\sum_{i}{t_s (c^{\dagger}_{iA} c_{iB} + c^{\dagger}_{iB} c_{iA})+t_l (c^{\dagger}_{iB} c_{(i+1)A} + c^{\dagger}_{(i+1)A} c_{iB})}
$$
where I have considered a one-dimensional problem. Since the distance between sites is not always the same, you might want to consider two different hopping parameters: $t_s$ for short jumps and $t_l$ for long ones.
EDIT: I had forgotten terms in the Hamiltonian, nearest neighbor hopping terms must be present in both ways $(A,i)\rightarrow (B,i)$ and $(B,i) \rightarrow(A,i)$. The long jumps are $(A,i+1)\rightarrow (B,i)$ and $(B,i)\rightarrow (A,i+1)$.
END EDIT
If you want to obtain a diagonal form for your Hamiltonian, you can try to find a $2\times2$ matrix $M$ such that:
$$
H=-\sum_{k}{(c^{\dagger}_{kA} c^{\dagger}_{kB})M\binom{c_{kA}}{c_{kB}}}
$$
$M$ will contain hopping parameters $t_s$ and $t_l$, once you have diagonalized $M$ your problem is solved.