The input panel's in Windows CE aren't loaded by any specific program, they're loaded by the OS itself (likely by GWES, but you'd have to walk the CE sources to verify that if you really, really want to know). The net result of that is that you can't set any "command line" in the debugger to get it to load your SIP. The downside is that you can't get use the debugger (you could use the Platform Builder debugger if it was generic Windows CE and you had a BSP).
To "register" your InputPanel, you simply need to create the approprate registry entries (documented in MSDN)
HKEY_CURRENT_USER\CLSID\{your object CLSID}
InprocServer32=reg_sz:"\\Windows\\mysiplib.dll"
IsSIPInputMethod=reg_sz:"1" ;note this is a string, not a dword
DefaultIcon=regsz:"\\Windows\\mysiplib.dll,0"
To get it to "appear", you probably have to go into the Control Panel, under Setings->Personal->Input.
Once loaded, you can't unload the SIP without removing the registry entries and then a soft reset.