Do we know how "smooth" was the dissolution of KGB? How significant was the initial overlap in personnel with the FSK and later FSB? Were the methods and role of KGB ever officially condemned by the new organizations (or the state)?

This is a question that is very difficult to answer within a twenty year time frame, because certain developments set in motion in 1991 did not reach fruition until the 2000s. I am almost entirely drawing from Soldatov and Borogan's The New Nobility, which is technically a piece of journalism but that sort of thing is neccesary given the topic, and they are generally considered the experts on the topic of the FSB.

The broad answer to your question of whether the transfer was smooth is is yes and no. The KGB was a very sprawling organization with an enormous amount of power that was still tightly controlled by the Communist Party (a feature that differentiates it from its successors). Its power, and the fact that its director was a key participant in the 1991 coup attempt, led Boris Yeltsin and his administration to be deeply suspicious of the organization, but the political uncertainty of the early 1990s meant he was also unwilling to really dissipate its power. So the KGB was broken up into a number of different organizations, such as the FSK/FSB, the largest and focused on counter espionage/counter terrorism, but also the FSV (focused on foreign intelligence) and the GUSP (focused on secret underground KGB projects, no joke). The KGB itself was hardly a model of internal harmony, and its power being divided among different organizations likewise did not produce harmony, particularly seeing as Yeltsin encouraged infighting and division to head off political challenge (for example, the FSK was in charge of counter espionage, but communications in general was handled by the FAPSI, so the two butted heads over jurisdiction and thus Yeltsin could benefit from their correspondence). This did not lead to particularly effective action, but Soldatov and Borogan frame this as a feature rather than a bug: the Soviet Communist Party had cells in virtually every level of KGB administration, which meant that no matter how powerful it got it could never escape political control. This was not possible in the liberal democratic political structure that Yeltsin sort of attempted to build, but as noted earlier he did not ant to actually give up the state's power. So he tried to use competition and mutual enmity as controls. In this way, the transfer was organizationally chaotic, very much unsmooth, but perhaps purposely so.

To step outside of the twenty year window a bit, the FSB later absorbed many of the KGB splinter departments. It would be very easy to attribute this to Vladimir Putin, ex-KGB, but the groundwork was laid at least as far back as 1995, when the FSK's problems were lay bare in Chechnya.

On a personal level it could also be very difficult. KGB officers were highly valued in Soviet society and entitled to apartments, pensions as well as general benefits accruing to the prestigious. The collapse of the Soviet system put this in jeopardy and many officers were forced to find work elsewhere--there is something of a cliched image of a ex-KGB officer working for a mobster or in an oligarch’s employ that was not entirely fictional. The 1990s were dangerous, even for the rich and powerful, and KGB officers were the best trained to deal with that. Ging from honored defenders of the state to gangster bodyguard is a bit of a step down in self esteem terms.

But to use another cliche, there is no such thing as a former KGB officer. Despite its rivalries it was a very close knit organization, even generationally--many KGB were the children of KGB. Adding to this, many of the former KGB were in fact so-called “active reserve” or undercover agents (although for sort of complicated bureaucratic details of pay many actually had greater ties to their new bosses). So while the KGB underwent wrenching organizational and personnel changes, the internal culture and camaraderie remained, Putin himself being a very good example of this, as he left the KGB in 1991 but, stepping outside of the twenty year rule, has clearly not forgotten the people there.

So the broad answer is that yes it was wrenching, but no the changes did not really provide a long term weakening of the security services. The details are within twenty years (hell, within one year), so I can only suggest you read Soldatov and Borogan’s book.