TLDR: If Bowles had managed to keep and hold San Marcos the first time he took it he could have held out
So here is the most detailed information I could find on what went on. There seem to be several turning points, I'm just going to go through them all and point out where minor things could have been different.
On 16 January 1792, Bowles with a large band of Creeks took over and looted the Panton, Leslie, and Co. store in San Marcos (St. Marks). He then tried to negotiate with the Spanish over the establishment of a Muskogee state. The Spaniards turned the tables on him and captured him instead.
If he hadn't been captured things could have turned out very differently, because of this he spends several years away, some of them in captivity.
But! He escapes and stops off in Britain:
While being returned to Spain, Bowles escaped and took charge of a ship to Africa, and eventually made his way back to Florida after stopovers in England and Nassau to regather his British supporters.
If the British had placed a greater value on Bowles and his disruptive actions against the Spanish and United states they could have supplied him with more support when he stopped in England - something the Spanish may not have been duely prepared for and if he had taken more land, key ports and such this could have changed the military capacity entirely. We do know that, with what support he had he hampered the Spanish for a while both at sea and eventually taking a Spanish fort.
Bowles finally came up with a successful plan to capture the fort and Panton-Leslie store at San Marcos.
However, naturally, the Spanish want it back.
On 23 June 1800, a large Spanish force sailed up the St. Marks River and recaptured San Marcos. Bowles escaped with his few white supporters who were left; the Indians had already gone home before the attack.
If at this point Bowles had been prepared for an attack and (maybe with more support from the British) sunk the Spanish before they reached him. This also could have changed the way things went. The losses incurred may make the Spanish think twice about chasing after him again. Instead we now have the Spanish with a large force sitting at San Marcos and specifically looking out for Bowles.
Bowles decides to annoy the United states as well, just to attract more attention. He makes the Muskogee state and demands the U.S return indian land.
The Spanish now march into his new state with a large force, intent on finishing him off.
On 17 August 1800, a well-armed force of 272 Spaniards and Mulattos set out to destroy Miccosukee. They ran into disaster from the beginning, and returned to San Marcos two days later. Even though Miccosukee was only 30 miles away, they did not have good guides and were unfamiliar with the area. On the first day they were only able to go 3 miles; not much of a surprise attack, and with only 6 days' rations. The soldiers were already over-heated and getting sick, and would be in very poor fighting condition by the time they reached Miccosukee.
If Bowles had sufficient scouts and forces he could have taken these sick and tired Spaniards and their weapons - the battle would have been much easier, considering Bowles had the Indians on his side, than confronting them later. And confront them later he did, to his cost:
On 5 January 1802, Bowles took a large force of Seminoles (Miccosukees), Negroes, white pirates, and deserted Spanish soldiers from Pensacola, and laid siege to San Marcos. They were a strong force and gave heavy fire, but would have been more deadly if they had cannons. Twice, one of the Spanish ships approached and destroyed a series of trenches dug by the Seminoles. The Spanish inside the fort were not in great enough number to attack Bowles, and could only defend the fort. The only thing that prevented Bowles from capturing San Marcos was heavy fire from the ships, and more ships arriving. Also, news was received that the war between Spain and England was over. The siege ended after about 10 days.
Well, a lot of that is self explanatory. If he had been given cannons by the British, if he had taken cannons from the invading Spaniards mentioned above, if his ships had sunk the Spanish before they sailed up the river. If he could have taken the fort before those ships arrived. If the war between Spain and England hadn't ended... This was the start of the end, any how:
Bowles was discredited when he failed to take San Marcos. Finally, on August 20, 1802, the neighboring Seminoles signed a peace treaty with the Spanish. Even Bowles' strongest supporter, Chief Kinache of Miccosukee, signed. Bowles' war with Spain failed, and he no longer had British support. Britain had declared peace with France and Spain, and now considered Bowles a troublemaker, his state an illusion, and his supporters nothing more than pirates. Spain started to blockade the coast and choke an important trading supply line of Bowles.
From here the Spanish and Americans gang up on him and, details aside, he didn't have much of a chance once he failed to take San Marcos.