@greekjgg
You have to get in contact with Thomann guitar department by e-mail. gitarre@thomann.de
Refere to this case and ask for a custom case with extra space for the pedals you have.
http://www.thomann.de/de/thon_effect_case_for_line_6_helix.htm?ref=search_rslt_helix_375295_2
They will give you the final price and you have to pay before they start production.
Unfortunately it takes about 4 weeks from order to shipment. :(