I'm Muslim, I use Md. as for Muhammad. So when submiting to journals, should I stick to the 2nd & 3rd names? I'm currently facing problems in submitting to arxiv.org which asks for only first and last names.
My advice is to use at least 3 names (including your surname) so that you will be uniquely identifiable. It probably doesn't matter if you do not use your first name unabbreviated. I know a few researchers whose names are of the form: C. Harry Kay. I also know of researchers who go by a single name (Robby, Arvind). So just fill in whatever names you want , abbreviated or not, into the first names field.
Make sure you use the same configuration of names for your entire career, so that all your papers can be linked to you (I made this mistake).