Buton, you were very lucky if you saw ships going through the locks at noon. Usually, the northbound (Atlantic bound) traffic stops about 11:00 as they change direction in the Canal. The next ships start arriving around between 2:00pm and 3:00pm.
If you want to go through the locks, I'd recommend the partial transit. A full transit is 8 hours or more. Personally, I think you'll get just as much value at the Miraflores Visitor's Center. I've "locked up" a couple of times with a friend who skippered tugboats at Gatun and then at Miraflores. It's best to get to the Visitor's Center soon after they open at 9:00am. If you're interested in lunch, there is a restaurant with a nice buffet and great views, on the balcony, of the locks.
My wife and I have stayed at the Country Inn and Suites Amador a few times. It is a nice hotel, with a good view of the mouth of the Canal and the Bridge of the Americas. It's a bit quieter than the hotels downtown or in Casco Viejo. The downsides are that it is far from anything other than Miraflores and Amador, and the restaurants on Amador are pretty mediocre. The on-site TGIFridays really sucks. Across the parking lot is the Balboa Yacht Club. It's interesting for a beer, but don't order any food unless you have first applied for Social Security. You can raise a family and retire before your meal comes.
My current favorite place to stay in Panama (City) is Torres de Alba. It's in the heart of the city, El Cangrejo district. The rooms are suites with full kitchens. You're walking distance to many good restaurants and sites. And, they have the best breakfast buffet included in the price of the room.
As for jungle hikes and seeing animals -- consider going to the zoo at Summit Park (Parque Nacional Soberanía). It's a good taxi ride out of the city. At the zoo, you'll see birds and animals indigenous to Panama ... the Harpy Eagle (makes our Bald Eagle look like a dwarf); jaguar, crocodile, monkeys, coatimundi, tapirs, parrots, macaws, etc.
Hiking in the jungle will involve taking an overpriced birding tour on the Pipeline Road or renting a car and driving to El Valle (90 minutes west of the city) or to Camino las Cruces, (20 minutes north of the city) on the Madden Dam Road AKA Old Forest Road.
Saludos and happy diving.