There is no official guide for multi-site installation.
However regarding configuration – basically anything which uses .htaccess directives such as the firewall rules, blacklist, and cookie based brute force can only be configured on the main site because a multisite installation uses a single .htaccess file. (These features will be hidden from subsites anyway)
The other general features can be configured individually on each subsite – eg, each subsite will probably want to use the rename login page brute force feature, or add a captcha etc
Therefore in summary:
if you wish to allow each subsite to configure the applicable security features such as renaming their own login page, adding captcha, changing DB prefix etc, then DO NOT network activate the aiowps plugin because otherwise the subsite admins will not be able to see the aiowps plugin menu. Simply activate the plugin on the individual subsites.