okay so i have resolved this issue using css at last i changed the default css of the divs i am defining....
the height i gave in site main according to my website need i know it can't be resolved like this but it can help for a little height sidebars.....
little helpful as for me ...
.site-main {
position: relative;
height:auto;
min-height:640px;
}
.site-main .content-area{
position:relative;
min-height:100px;
height:auto;
}
.site-main .sidebar-container {
height: 0;
position: absolute;
top: 40px;
width: 100%;
z-index: 1;
}