Bowser is usually not very good against other amiibo, and is one of the harder amiibo to train, but Bowser can become a monster if you train him right.
Bowser amiibo have a few problems that make them harder to train. First, it is very easy to make them spam their side special and grabs. Second, they usually aren't very good with their final smash. With Bowser`s final smash, it is usually best to use your side smash, but it`s hard for Bowser amiibo to learn this. Also, try not to use your grabs and side special very much, unless you want those to be the only thing that it does.
When any amiibo nears level 50, their attack power is multiplied by 1.5, and their damage taken is multiplied by 0.5. The power and defence multiplier is added to his stats AFTER he receives his boosts from equipment. So a very defensive amiibo will be even more defensive near level 50, and the same thing with powerful amiibo. This greatly helps Bowser amiibo, as they are knocked off of the edge less, and they are EXTREMELY powerful. One forward air from a Bowser amiibo near level 50 can destroy Olimar`s Pikmin in one hit. At level 50, combos from a Bowser amiibo, even with his weakest attacks, can do tons of damage.
If your Bowser amiibo uses its side special too much, give it the custom special Dash Slash. It removes the grab part, and discourages Bowser amiibo from using it so much. But this doesn't change his side special during his final smash, so if the Bowser amiibo was using side special a lot, then it will use side special a lot during its final smash. Bowser's grabs can be useful, but make sure not do overuse them, as Bowser amiibo usually use their grabs more than other amiibo.
Bowser amiibo benefit from power and speed equipment the most. Bowser is already very heavy, so he doesn't really need defence equipment. Equipment with autoheal, life steal, or other effects that heal him are good too.
Bowser amiibo are hard to train, but are extremely good at time battles. They aren't as good at stock battles or 8-player smash, but they can still be good.