Byzantine military fortunes began to decline around 1059 A.D., and kept declining until Alexios I Komnenos managed to stabilize things around 1090. But even Alexios lost a lot of battles. It seems like he stopped losing battles when he decided to fight more conservatively.
But Alexios's heirs, John II and his son Manuel, abandoned that playbook. They took their armies on risky marches deep into enemy territory, and it regularly paid off. Both recaptured forts and cities in a way their predecessors seemed unable to do. Their troops seemed way more disciplined and rarely routed, even when situations were tough.
If you read Byzantine military accounts from the previous period, Byzantine troops regularly routed when surprised or faced with horse archer-based armies. That doesn't seem to happen much under these two.
Also, their success in siege warfare was remarkable. Both suffered some losses, but they won far more than they lost.
Questions:
So to answer this question, first we need to look at the structure of how the Romans recruited soldiers in this period.
The Themata or "Theme System" commonly espoused was the basis for Roman military service and pay prior to the Komnenian Dynasty, and one that continued as late as the Palaiologian Era. This might confuse some people because the general view is that the "Theme System" was a combined military-administrative district or "province" when that really wasn't the case. Basically, what the Romans did (this is something I am espousing in my Master's Thesis and plan to do my full Ph.D. on) was adapt the system used to pay foederati in late Antiquity to the rest of their army during the 7th century. While soldiers were still recruited through a mix of hereditary family obligations from Diocletian's laws, direct conscription, and volunteers, they were now typically paid with funds coming from inalienable lands known as stratiotika ktemata, which were holdings directly designated to provide tax revenue for funding an individual recruit. Soldiers did not own or work these lands, in fact they were barred from performing non-military labor and commerce by laws of Constantine VII, just as they always had been since the Roman Principate.
There were two problems that led to the demise of the Themata and a need for a replacement. The first was that beginning in 1034, the currency began to be debased, with the stable, almost pure gold nomisma which had been in circulation since it was first issued under Diocletian in 301 reduced from 24 Karats to 3 Karats or less by the coronation of Alexios I Komnenos in 1081. This caused rampant inflation, and more importantly devalued the pay of the military. The standard 2 to 4 nomismata plus payments-in-kind per annum that soldiers received was worth only a third of what it had been by the time of the Battle of Mantzikert, regardless of Roman laws about currency exchange rates, which meant that soldiers had less money to pay for equipment, rations, animals and servants, and other things they needed to serve as soldiers. It also increased the burden on families trying to provide the funds for initial recruitment, and decreased the value of the taxes coming from the stratiotika ktemata which were supposed to maintain that recruit's annual pay.
The second was that much of the stratiotika ktemata had been lost with the disarray in Anatolia. And while these lands and revenue streams would be reinstated as they were regained, a new system of exacting revenue was needed in the interim.
The Komnenoi addressed both of these problems about 10 years into the reign of Alexios I. In 1092 they introduced the hyperpyron to replace the nomisma, which was initially 20.5 Karats and would stay stable until the Fourth Crusade in 1204, after which it began to be debased. With a reliable currency in circulation again, this stabilized prices and the Army's ability to equip itself.
Alexios was also responsible for the introduction of the pronoia, which functioned similarly to the themata. With the pronoia, a pronoetes was given the right to the income stream from an allocation of taxable lands, in exchange for their service in the strateia (as a bureaucrat, soldier, or what have you). In exchange they were expected to use this income for their job as well as their own pay, which meant taking care of administration, infrastructure, and military forces in the region they were placed over. This system was far more similar to the traditional view of the Theme system, but still lacked the traditional "farmer-soldier," and the income of the Stratiotika Ktemata was still inalienable and still went directly to the individual soldiers they funded. But the pronoiarios was now the person funneling recruits to the imperial army, and in control of their pay.
(1/?) (Will continue when I get back from Lunch)