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How often should I stop to see if he needs to go potty?
I have a travel crate. Should I put him on the passenger seat or on the floor in front of it?
How often to rotate toys so he doesn't get bored with them?
Are fingernail-sized treats too big? I'd like to use string cheese.
Just about all my neighbors all have dogs. One or two sometimes bark when a person walks by (we're next to a trail). I don't want Migo to learn to bark when people walk by more than once or twice (I understand that Havanese are good "watch" dogs). Is training going to be more difficult because of the other dogs? They might bark at us when I take him outside. I don't plan on coddling him, but I don't want him to become scared of other dogs either. Should I take him somewhere else to potty?
The trip for two of mine was 2 ours to the airport, 3 hours of airport/flight time, and another 1 1/2 hours home from the airport. For the car ride parts, I only stopped when they fussed and acted like they needed to go. Kodi fussed at about the half way mark, Pixel made it all the way to the airport. At the airport, I gave both of them an opportunity to potty. In Kodi's case, we found an empty gate, and just put his pee pad on the floor for him. (which he had no interest in at that point) Pixel, who hadn't peed on the trip to the airport did need to pee. There were some big planters with fir trees in them, up off the ground. I plopped her in one of those and she promptly went.

Both peed at the end of the flight home... Again, we just found a quiet corner and plopped them on a pee pad. They were fine the rest of the way home.
The SAFEST place for the crate is on the floor of the back seat. Second safest place is on the back seat, belted in, so the crate can't get thrown around. If you MUST have the puppy in the front seat, put the crate on the seat, MAKE SURE the air bag is disengaged, and seat belt the crate securely in place. Without the airbag disengaged, ANYPLACE in the front seat is an almost sure death-trap for a puppy in an accident that makes the airbags deploy.
I was not very scientific about toy rotation, and I'm still not. When I see toys are being left around and not engaged with, I put them away in a separate toy bin. Every few weeks, I let them rummage in the "extra" toy bin. They act like it's their long-lost best friend when they "find" a toy they haven't seen in a while.
When you are talking about treats, I hope you aren't talking about on the way home? I wouldn't feed him ANYTHING during travel.
I also don't give trees "just because". They each get a piece of something freeze dried (or dehydrated) at bed-time. Otherwise, ALL treats are training treats. Since I do a lot of training, I want their training treats to be solid nutritionally. So, when they were tiny, I used a lot of boiled chicken. As they got older and tummies became used to more things, I use all kinds of cubed, lean, roasted meat. OCCASIONALLY I will use a low fat string cheese cut in small pieces for the girls. (Kodi is dairy intolerant) But I limit cheese because it is quite rich, and in large quantities can lead to pancreatitis in small dogs. Another food I often use for training treats when I don't have time to cook is Fresh Pet. (in a refrigerated case in many grocery stores, big-box pet stores and Target) It comes in a form that is small, soft pellets. I actually cut each of these pellets in half for the adult Havanese... If you have the patience, you could quarter them for a young puppy... or just break them apart with a fingernail on the fly.