there is no magical solution to this problem. you have two choices:
a) relocate the fuse box under the battery. difficult to do on an ATX due to clearance issues, and difficult to troubleshoot if something does go wrong
b) do the right thing, and relocate your battery to the trunk, and then you can move your fusebox to the location where you battery used to be
I still don't understand why everyone doesn't relocate there battery to the trunk

, it makes everything so much easier to service things under the hood and it helps create a much better weight distribution (50:50 is deal, front wheel drive cars are too heavy up front...)