I can think of at least a few roles protos can play when integrating with BA:
Blocking/Fixing for Anti-Mech Attacks -- BA often have trouble catching enemy mechs for anti-mech attacks. But a single proto can block an enemy mech or vehicle's movement into a hex. Thus a point of smaller, faster protos can surround a mech or vehicle, fixing it in place for coup de grace anti-mech (swarm or leg) attacks by BA point. Seemingly worthless small or poorly armed protos can be surprisingly good in this role due to their low BV.
"Heavy" Cavalry -- Heavier, slower BA points defending fixed positions (think Golem points) can become isolated or outranged. Relatively mobile protos with decent firepower, like the Roc, Gorgon 2, Delphyne, and Procyon Quad can serve as a mobile reserve, covering multiple BA defensive positions and reinforcing them depending on which BA position is getting hit hardest.
Fire Support -- Some protos like the Gorgon, Minotaur 3, and Svartalfa carry large LRM racks. A point of them can throw as many or more missiles than a heavy or assault mech or tank. BA can spot for indirect fire from these fire support protos, or the protos can just fire directly from behind the BA.
Special Munitions Support -- Some protos like the Orc, Centaur, Hippogriff, and Sprite carry multiple small SRM or LRM racks. These can be used as flexible force multipliers, delivering inferno, flechette, minelaying, smoke, and other special munitions as needed to enhance the attacks or defenses of allied BA.
E/W Support -- The Satyr's light probe can sweep out areas more than twice as fast as most BA and identify hidden enemy units that need flushing by allied BA. Similarly, if Arrow IV artillery is available, the Satyr 4 (my only canon design) can more easily keep its light TAG trained on enemy units than slower BA with the light TAG.
Some Society protos like the Basilisk Quad and Boggart get into more exotic roles like physical, electrical, and incendiary attacks that are worth considering if playing the Society (or for homegrown designs).
Finally, upthread GreekFire should have plugged his series on proto tactics and his proto reviews. They're required proto reading. Here's links to his first articles for each:
https://bg.battletech.com/forums/index.php?topic=43037.msg993154#msg993154https://bg.battletech.com/forums/index.php?topic=20928.0Hope this helps.