I think the general approach is like this:
First, Upload your new logo in iv-config folder, say it's 100x100px mylogo.png. We need to add 9px for the sides of the logo that will give the 118x118px overall size. Imagevue can use smaller logo for inner pages but we will override this too.
Open Settings > Custom CSS > HTML and paste this:
/* Change 118px to your height+18px in these two lines: */
#logo, .inner #logo, #pageHeader a.logo, .inner #pageHeader a.logo { height: 118px; line-height: 118px; }
#tree #hidden { top: 118px !important; margin-top: -9px; }
/* Change 118px to your width+18px in the next line and make sure the path is correct */
#logo, .inner #logo { width: 118px; display: block; background: url(/iv-config/mylogo.png) 9px 9px no-repeat; }
.inner #pageHeader a.logo { margin-left: 9px }
For your logo you will have to change the sizes accordingly.