Is there any advantage of BS/MS (masters without thesis though) over BS (in engineering) while applying for a PhD.  I would really appreciate honest suggestions. I am asking this because I chose the former and GPA has gone really down due to large amount of course work and at this point I am worried about getting a good grad school for PhD.

There is definitely an advantage of having the MS thesis. It is because that you will have some experience of the research. I would prefer for MS thesis and if possible some publication in like IEEE during your MS study or thesis. After doing this (+good GRE ) you will be a good candidate for your PhD admission.