I don't know the precise answer to your question and you probably have more experience formatting in your native language.
My guess is that doing a conversion from DOCX to Kindle or DOCX to epub will be horrible. MS Office will probably specify its own font, and then Kindle won't support it or allow it to be embedded.
Here is a better strategy. Focus on producing an epub file which validates as EPUB 3 http://validator.idpf.org/ If it validates, my guess is that it will also render easily on Kindle if you convert from epub to Kindle using Kindle Beta Previewer. https://www.amazon.com/gp/feature.html?docId=1003018611
The work processes (and the necessary steps) for producing a kindle/epub file are a lot different for creating a Createspace printed book. What works in Createspace will probably not work for Kindle and vice versa.
To produce a good epub/kindle file, you should probably create the content using an HTML/epub editor. Try using either of these two (free) products:
Calibre's EPUB editor (which is different from the Calibre
conversion part). See https://manual.calibre-ebook.com/edit.html
sigil epub editor.
The one thing I do not know is if the included Kindle fonts include support for Malayam characters. If you have heard that they do, then it should be easy.
If not, then you will have to embed a special Malayam font yourself. This is not extremely difficult, but it is complicated. See https://kindlegen.s3.amazonaws.com/AmazonKindlePublishingGuidelines.pdf Chapter 9 .
Good luck, and try to tell us what worked for you!