As Keerthi Madapusi Pera points out in his comments, it is certainly reasonable to define a unipotent flat vector bundle as a flat vector bundle that is a successive extension of the trivial one $(\mathcal O_X,d)$. Over a general basis $S$ I don't know, but over a field there are plenty of references.

For instance let $k$ be a field of characteristic zero and $X$ a smooth geometrically connected scheme over $k$. Then according to

Deligne, P.
Le groupe fondamental de la droite projective moins trois points.

http://www.math.ias.edu/files/deligne/GaloisGroups.pdf

$\S$ 10.26 the category of unipotent flat vector bundles over $X$ is even Tannakian (a fortiori abelian), giving rise to the "De Rham fundamental group" $\pi(X,x)_{DR}$.

If you want to work in positive characteristic, or with singularities, flat vector bundles are certainly not the right objects any longer (at least if you want to have some link with the fundamental group), one has to replace them with stratifications, see

Saavedra Rivano, Neantro Catégories Tannakiennes.
Lecture Notes in Mathematics, Vol. 265.

http://www.springerlink.com/content/w141370u7g5u/

VI 1.2

or

dos Santos, João Pedro Pinto
Fundamental group schemes for stratified sheaves
J. Algebra 317 (2007), no. 2, 691–713.

http://www.sciencedirect.com/science/article/pii/S0021869307001640

One could also mention that over a complete scheme over a field, you don't need to consider connexions at all. For instance Nori in chapter IV of his phd

Nori, Madhav V.
The fundamental group-scheme.
Proc. Indian Acad. Sci. Math. Sci. 91 (1982), no. 2, 73–122.

http://www.springerlink.com/content/x246hl378t2737p5/

considers a scheme of finite type $X$ over a field $k$ such that $H^0(X,\mathcal O_X)=k$, and proceeds to show that the category of unipotent vector bundles is indeed Tannakian (the explanation is that one can deduce from this that unipotent vector bundles are in fact endowed with connections). Lemma 2 there may be of interest for you, because he shows exactly the abelianness in this similar context.