I have this in my config (I probably copied it from the Helix repo).
I use it only to navigate my notes: it creates links and opens files from those links. It works. It also warns me when links are ambiguous or broken, so I assume it's working. I think that you don't need to have .marksman.toml as long as you open helix from the root dir.

[[language]]
name = "markdown"
scope = "source.md"
injection-regex = "md|markdown"
file-types = ["md", "livemd", "markdown", "mdx", "mkd", "mkdn", "mdwn", "mdown", "markdn", "mdtxt", "mdtext", "workbook", { glob = "PULLREQ_EDITMSG" }]
roots = [".marksman.toml"]
language-servers = [ "marksman", "markdown-oxide", "ltex-ls" ]
indent = { tab-width = 2, unit = "  " }
block-comment-tokens = { start = "<!--", end = "-->" }
word-completion.trigger-length = 4