What is known about Higgs bundles with sections? Let $C$ be a complex curve.  Recall that a Higgs bundle on $C$ is a vector bundle $E$ on $C$ equipped with a morphism $E \to E \otimes K_C$.  The space of (stable) Higgs bundles is much studied, and is in particular known to be smooth.  Moreover there is a "nonabelian Hodge theorem" giving a diffeomorphism between the moduli of Higgs bundles and a certain character variety of $\pi_1(C)$. 

What is known about the moduli space of Higgs bundles with a section, i.e., the space parameterizing triples $(E, s \in \mathrm{H}^{0}(E), \phi: E\to E \otimes K_C)$ ?   Is it smooth (after imposing some appropriate stability condition)?  Is there an analogue of the "nonabelian Hodge theorem"?

 A: There is a fundamental difference between the case of Higgs bundles (where the section lies in a twisted adjoint representation) and the case of a section of the bundle itself (where the section is in the vector representation).  In the former, the notion of stability is rigid, whereas in the latter the definition of stability depends on a parameter.  This was discovered by Bradlow (J. Differential Geom. 33 (1991), no. 1, 169--213) and Bradlow-Daskalopoulos (Internat. J. Math. 2 (1991), no. 5, 477--513) and exploited by Thaddeus (Invent. Math. 117, no. 2 (1994),  317--353).  These papers will point you in the direction of a definition of stability/semistability for the case you're interested in.  I guess it will be true that stable points are smooth, though for certain values of the parameter  the compactifications will contain strictly semistable (non-smooth) points.
To answer your question, there is apparently no relationship between Bradlow pairs and representations of the fundamental group.  Rather, these spaces are more closely related to higher rank generalizations of symmetric products of the Riemann surface (see also J. Amer. Math. Soc. 9 (1996), 529-571). 
A: For stable $E$ of degree $0$ there are no nonzero holomorphic sections. The interessting things must happen at non-stable bundles.
As far as I know, there is a desingulaization procedure for the space of semistable holomorphic bundles $V$ similar to your situation: one takes $E=End V$ together with a holomorphic section of $E.$ Again, in the case of stable bundles there are only multiples of the identity, but for nonstable there are more endomorphisms.
For details, see Tyurin#s 'red book' on vector bundles over surfaces (Quantization, Classical and Quantum Field Theory and Theta functions) and the references therein. Maybe you can apply these ideas to your situation.
A: Comment to Sebastian answer 
If the stable vector bundle $E$ be of negative degree then there is no non-zero holomorphic sections due to Kobayashi and also Wu. A non-zero holomorphic section of a vector bundle $E$ on $X$ gives an injective homomorphism from $\mathcal O_X$ to $E$. So, the image of this homomorphism is of degree zero but the stable vector bundle $E$ has negative degree.
Line bundles with zero degree admit non non-zero holomorphic section.
From Kobayshi In general for stable vector bundles with zero degree all the holomorphic sections are parallel
About your question I don't think such moduli space be smooth in general.
Let $X$ be a complex affine scheme, it is said to have quadratic algebraic
singularities if it is defined by finitely many quadratic homogeneous polynomials. Let $X$ be an analytic space, it is said to have quadratic algebraic singularities if it is
locally isomorphic to complex affine schemes with quadratic algebraic singularities.
We know from the following work of Nadel
Nadel, Alan Michael
Singularities and Kodaira dimension of the moduli space of flat Hermitian-Yang-Mills connections
Compositio Mathematica, Volume 67 (1988) no. 2 , p. 121-128
moduli space of flat locally free sheaves on a compact complex Kahler manifold which are stable have quadratic algebraic singularities.
Nadel showed that the Moduli space of Hermitian-Einstein metric on stable vector bundles have quadratic algebraic singularites,
So I guess you must work on such type singularites for your moduli space of Higgs bundles with a section
