The covariant formalism is a bit tricky. The problem is that you cannot use the proper time directly in the Lagrangian, because it implicitly contains the constraint that [itex]\mathrm{d} \tau=\mathrm{d} t \sqrt{1-v^2}[/itex] (I'm setting the speed of light to 1 here).
You can, however use an arbitrary "world parameter" and write down a parameter-independent action functional. For the free particle it's
[tex]S_0[x]=-m \int \mathrm{d} \lambda \sqrt{\dot{x}_{\mu} \dot{x}^{\mu}}.[/tex]
I'm using the "west-coast convention" for the pseudometric, i.e., [itex]\eta_{\mu \nu}=\text{diag}(1,-1,-1,-1)[/itex].
The interaction with an external electromagnetic field is determined by
[tex]S_i[x]=-q \int \mathrm{d} \lambda \dot{x}^{\mu} A_{\mu}(x).[/tex]
Note that the total Lagrangian,
[tex]L=-m \sqrt{\dot{x}_{\mu} \dot{x}^{\mu}} - q \dot{x}^{\mu} A_{\mu}(x)[/tex]
is a homogeneous function of degree 1 wrt. [itex]\dot{x}[/itex]. This implies the parameter independence. Now you can derive the equations of motion from the Hamilton principle of least action as usual, using the Euler-Lagrange equations. The canonical momenta are given by
[tex]p_{\mu}=\frac{\partial L}{\partial \dot{x}^{\mu}}=-m \frac{\dot{x}_{\mu}}{\sqrt{\dot{x}_{\nu} \dot{x}^{\nu}}}-q A_{\mu}[/tex]
and thus the equation of motion
[tex]\dot{p}_{\mu}=\frac{\partial L}{\partial x^{\mu}} \; \Rightarrow \; -m \frac{\mathrm{d}}{\mathrm{d} \lambda} \left (\frac{\dot{x}_{\mu}}{\sqrt{\dot{x}_{\nu} \dot{x}^{\nu}}} \right ) - q \dot{x}^{\nu} \partial_{\nu} A_{\mu}(x)=-q \dot{x}^{\nu} \partial_{\mu} A_{\nu}.[/tex]
Now you can bring this into a more familiar form by rearranging the terms to
[tex]m \frac{\mathrm{d}}{\mathrm{d} \lambda} \left (\frac{\dot{x}_{\mu}}{\sqrt{\dot{x}_{\nu} \dot{x}^{\nu}}} \right ) = q \dot{x}^{\nu} (\partial_{\mu} A_{\nu}-\partial_{\nu} A_{\mu})=q F_{\mu \nu} \dot{x}^{\nu}.[/tex]
Now you can choose for [itex]\lambda[/itex] whatever parameter you like. It is crucial to note that the equation of motion, if derived from a Lagrangian that is homogeneous in [itex]\dot{x}^{\mu}[/itex] of degree one, automatically fulfills the constraint equation
[tex]\dot{x}^{\mu} \frac{\mathrm{d}}{\mathrm{d} \lambda} \left (\frac{\dot{x}_{\mu}}{\sqrt{\dot{x}_{\nu} \dot{x}^{\nu}}} \right )=0,[/tex]
which implies that the 4 equations of motion are not independent from each other and thus you can choose the parameter [itex]\lambda[/itex] as you like after the variation is done, i.e., on the level of the equations of motion.
If you choose the proper time, [itex]\lambda=\tau[/itex], then you get [itex]\dot{x}_{\mu} \dot{x}^{\mu}=1[/itex] and thus
[tex]m \frac{\mathrm{d} u_{\mu}}{\mathrm{d} \tau}=q F_{\mu \nu} u^{\nu} \quad \text{with} \quad u^{\mu}=m \frac{\mathrm{d} x^{\mu}}{\mathrm{d} \tau}.[/tex]
You can as well chose a coordinate time, [itex]t[/itex] of an inertial frame. Then the equation of motion appears in a form that is not longer manifestly covariant, but you get, because of [tex]\dot{x}^{\mu} \dot{x}_{\nu}=1-\vec{v}^2, \quad \vec{v}=\frac{\mathrm{d} \vec{x}}{\mathrm{d} t},[/tex]
for the spatial part of the equations of motion (writing the Faraday tensor in terms of the three-dimensional notation with [itex]\vec{E}[/itex] and [itex]\vec{B}[/itex])
[tex]m \frac{\mathrm{d}}{\mathrm{d} t} \left (\frac{\vec{v}}{\sqrt{1-\vec{v}^2}} \right ) = q (\vec{E}+\vec{v} \times \vec{B}),[/tex]
and the time component is just the energy-work relation, following from this:
[tex]m \frac{\mathrm{d}}{\mathrm{d} t} \left (\frac{1}{\sqrt{1-\vec{v}^2}} \right ) = \vec{v} \cdot \vec{E}.[/tex]