Pemalink structure for separate BuddyPress install on a subdomain

In order for me to better manage my BuddyPress and website, I have decided to go ahead and install BuddyPress with a second instance of WordPress on a subdomain. I understand that I will need to manage that 2nd installation of WordPress separately with Plugins, etc., but I am hoping to find an answer to my permalink question. Should my permalink structure in the second installation of WordPress with BuddyPress match the permalink structure of my main site. For example on my main site, my permalink structure is /%year%/%category%/%postname%/. Should this same structure exist or does this matter?