Unfortunately I passed on to my children crummy genetics WRT allergy and sinus problems! We've dealt with lots of sinus and ear issues. My son eventually had tubes. It was the route I wanted to go, but I'm so glad we did! He'd lost some hearing, but within a week of the tubes, he was like a different person.
Definitely use a good probiotic to help with good bacteria, or you can end up with other problems.
I tend to have a lot of excess fluid in my ears (a fairly new occurrence for me), and it's very painful. I use a neti pot, which is great but unlikely on a 13MO (great for adults and older children, though!). I do lots of head/neck massages for myself and DC, and that works to get the fluid moving. When their sinuses are acting up, I will massage their heads every hour or two so that we can keep things moving along.
I also use mild heat and hot showers (baths for DC). The trick is to get the extra fluid out instead of treating the infection, which is backwards from the way doctors handle the problem. The fluid sits without moving and becoming a breeding ground for bacteria (think: stagnant pond).
By treating with antibiotics, you're just getting rid of the bacteria, which is fine, but if you never get rid of the fluid, the infection will keep coming back. (Plus, the build-up of fluid is what causes the hearing problems and not necessarily the infection.) So the first step I'd take is to get rid of the fluid.
We also use Auro drops. They're chamomile. You put them in, and they numb the eardrum for a short period - wonderful for pain relief to get to sleep. I also had at one point (but unfortunately lost the contact info) an herbal sinus remedy I bought from someone locally. I think it was peppermint & eucalyptus. She'd put it in a bottle with a roll top, and you just rolled it behind your ears. That worked really well to open up my Eustachian tubes, and it was pretty inexpensive - $10 for a bottle that lasted all winter.