When I open up a file in IDA Pro, I usually want the HexRays decompiler panel to the right of the disassembly. It just so happens that I open up a lot of files in IDA Pro and I have to rearrange the panels every time. Now I finally sat down and wrote a little Python plugin that will rearrange the panels just the way I like them. You may have similar problems and may find it useful. You should be able (with only a small amount of pain) to modify the script according to your own preferred layout:
import idaapi

def runonce(function):
    A decorator which makes a function run only once.
    function._first_run = True
    def wrapper(*args, **kwargs):
        if function._first_run:
            function._first_run = False
            return function(*args, **kwargs)
    return wrapper

def position_pseudocode():
    idaapi.set_dock_pos('Pseudocode-A', None, idaapi.DP_RIGHT)
    idaapi.set_dock_pos('Graph overview', 'Output window', idaapi.DP_TAB)
    idaapi.set_dock_pos('Functions window', 'Output window', idaapi.DP_TAB)

class PseudoCodeTabRight(idaapi.plugin_t):
    flags = idaapi.PLUGIN_HIDE
    comment = 'Opens the PseudoCode tab in a spearate pane to the right.'
    help = 'The plugin triggers automatically when the decompiler is engaged for the first time.'
    wanted_name = 'PseudoCodeTabRight'
    wanted_hotkey = ''

    def init(self):
        def hexrays_event_callback(event, *args):
            if event == idaapi.hxe_open_pseudocode:
            return 0
        if not idaapi.install_hexrays_callback(hexrays_event_callback):
            return idaapi.PLUGIN_SKIP
        return idaapi.PLUGIN_KEEP

    def run(self, arg=0):

    def term(self):

    return PseudoCodeTabRight()