Hello,
1) You should be able to adjust the cart position in the floating menu bar below. The logos appear identical in alignment for me.
Template.CSS - Line 653
#s5_menu_wrap.s5_wrap_fmfullwidth #s5_cartbutton {
margin-right: 14px;
}
2) You can publish another module to the popup by using the s5_box1 position in the Module Manager. By default we just have some text there to illustrate this purpose.
3) Are you using the S5 Register Module to login?