To link to or from a SubPage, you can normally use a regular WikiLink that does not contain the name of the parent directory of the SubPage. Ikiwiki descends the directory hierarchy looking for a page that matches your link.
For example, if ?FooBar/SubPage links to "OtherPage", ikiwiki will first prefer pointing the link to ?FooBar/SubPage/OtherPage if it exists, next to ?FooBar/OtherPage and finally to ?OtherPage in the root of the wiki.
Note that this means that if a link on ?FooBar/SomePage to "OtherPage" currently links to ?OtherPage, in the root of the wiki, and ?FooBar/OtherPage is created, the link will change to point to ?FooBar/OtherPage. On the other hand, a link from ?BazBar to "OtherPage" would be unchanged by this creation of a SubPage of ?FooBar.
You can also specify a link that contains a directory name, like "FooBar/OtherPage" to more exactly specify what page to link to. This is the only way to link to an unrelated SubPage.
You can use this to, for example, to link from ?BazBar to "FooBar/SubPage", or from ?BazBar/SubPage to "FooBar/SubPage".