I know that there are examples of paintings and sculptures, but were there any manuscripts or books that took elements of indigenous religions and wove them into Christianity?
You may be interested in looking at the books called the “Testerian Catechisms”, some of the earliest European style books in the Americas. These 16th century books were meant to help with the indoctrination of indigenous communities in Central Mexico before religious instructors began to learn native languages. Because of the lack of linguistic understanding, the Testerian books used pictorial stories to describe basic biblical narratives.
It's important to remember that as far as literature goes, there wasn't a whole lot produced before independence. In the case of New Spain (Mexico), that was because Spain banned the importation and production of novels. So what passes for lit in the colonial era is mostly poetry, travel logs, plays and cartas de costumbres - stories about local traditions.
An interesting early example is Siguenza y Gongoras Theatre of Political Virtues which extols the Aztec role in the founding of Mexico City, which really wasn't done at that time. It's from the 1690s - he was a contemporary and friend of Sor Juana.
The 19th century saw the rise of national romances, many of which ignored the Indian question entirely. One of the few who didn't was Ignacio Altamirano (Mexico) who was indigenous himself. I'm working on an article about his Christmas in the Mountains right now.
The 20th century is when you see the true risen of indigenismo and syncretism. There are innumerable examples, but my favorites are Rosario Castellanos' Balun Canan (Chiapas) and José Maria Arguedas' The fox above and the fox below.