The answer you're looking for can be summed up in a single sentence: Think about how wild Pokémon would battle.
See, it's not unusual for a Pokémon to use itself as the only combatant, and it's equally not unusual for a battle to be less than a one-on-one match. (Six-on-six technically isn't even all that traditional. Think about how many trainers in the games or the anime use their full roster against another trainer. That kind of thing is usually reserved for special battles; most of the trainers in either canon carry around less than that, while the game's hero avatar usually only needs a handful to take out NPCs.) So, for a Pokémorph battle, all you need to do is think about how one of these wild Pokémon would engage in battle with others. Sure, the Pokémon in question would have a human mind, but other than that (and, of course, differences in the way a morph's body would work compared to the way a full Pokémon's body attacks), it's pretty much the same.
In terms of strategy, yes, it'd be different. If your story takes place only a little while after the virus hits, people will probably be incredibly cautious when it comes to a match unless you're trying to say something about their general character. After all, they've got only one shot at winning. They can't simply switch in another Pokémon when the going gets tough. Most of all, they're directly involved in all the danger. Although Pokémon battling's a huge sport, I'm not sure how many people would readily jump into a Rock Slide themselves.
Of course, you could potentially have a tag-team battle happen, where morphs team up with other morphs to fight. Some might even "switch in" if the single opponent they're battling happens to have advantages over them. Professional wrestling actually does this kind of thing a lot. It might give you some ideas on how to go about doing it.
Other than that, the concept's pretty vague. A lot of people write about morphs in a war of one kind or another, but you could be cooking up something that puts a new spin on the genre. *shrug* Good luck.