publications - Academic affiliation: which to choose?

I am actually working for two different universities in my country, and the problem is that they do not give too much support to academic research. I mean for paying the costs of tickets, travel expenses or accommodation when one paper get accepted for a conference.

I usually work as an independent researcher, but the problem that I have is that if I put my author affiliation as Independent researcher maybe I will be not be considered "serious" enough for the reviewing program committee of the conferences that I plan to submit my work.

Now what should I do? should I put the name of one of the universities that I am working at random, and at the end change my affiliation and put the name of the university that will give me the funds for the travelling expenses of the presentation?

What would we the best way to act in this way? I remember that for one paper that I was submitting, the Dean of my past faculty told me that he could give me the money, but if I put him like a co-author. Actually it was his way to get publications to his name without working on them. Of course, I did not accept that.

Any suggestion would be of great help

Thanks