Yes, you can apply patches from (mostly) any source. There'd be a slightly different markup/setup depending on how you popoulate your stackage/hackage - nix or http_archive (stack_snapshot). If you're modifying something from an upstream it'd be best to reference it as vendored, e.g. `@org//:package` and not the stack populated version `@stack//:package`. This is how you'd do it pulling from git directly (there's a whole lot more involved if this were to be done for a stackage package).

    http_archive(
        name = ...,
        build_file_content = """
          load(
            "@org//bazel:defs.bzl",
            "pai_haskell_library",
          )

          pai_haskell_library(
            name = ...,
            version = ...,
            srcs = glob(["src/**/*.hs"]),
            stackage_deps = [...],
            visibility = ["//visibility:public"]
          )
        """,
        patch_args = ["-p1"],
        patches = [
            "//dir:git-patch-file",
        ],
        sha256 = "...",
        urls = ["https://github.com/org/repo/archive/1.0.0.0.tar.gz"],
    )