Yes, you should edit the "skin/common_files/modules/Product_Options/customer_options.tpl" template.
Find and replace this code:
Code:
{if $o.modifier_type ne '%'}
{currency value=$o.price_modifier display_sign=1 plain_text_message=1}
{else}
{$o.price_modifier}%
{/if}
with this:
Code:
{if $o.modifier_type ne '%'}
{currency value=$o.price_modifier display_sign=1 plain_text_message=1}
{else}
{if $o.price_modifier lt 0}
{$o.price_modifier}%
{else}
+{$o.price_modifier}%
{/if}
{/if}