
Cevah |

To position it, you must command it in a language it understands. Since they are usually animals, you need Speak with Animals active. Otherwise, they act as uncontrolled creatures that attack the nearest enemy of yours. The magic does that for you. Fine details require communication. Handle Animal can maybe help, but that is GM call territory.
/cevah

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Cevah,
Since you can summon it in any of a number of squares, doing a good initial placement on the summoned creature should make it fairly easy to use it as a flanking partner.
After all, if it appears next to the creature you want flanking on, on the opposite side from where you (or the person you are using it to give flanking to), there shouldn't be any need to even be able to speak to it.
Close range gives you 25' or more of distance from you to summon it in.
But, to answer the OP, yes, unless something else happens, your summoned creatures usually count as your allies, and your allies' allies, so a dog, as an example, summoned via SNA or SM will serve as a flanking partner for your ally the Rogue who is on the opposite side of the enemy from your dog.
There are a few things that can change that, including spells that can cause your creature to befriend the enemy....

Cevah |

Sure, initial position is easy. The OP mentioned commanding into position, however. That needs language.
What happens as the battlefield changes? An uncontrolled summons moves in a strait line to the nearest square where they can attack. This may not be a square that flanks the enemy with an ally.
/cevah