I personally I think a good C/O doesn't necessarily need to instruct each individual squad on where to go - Its really up to the squad leaders to decide on which flags they want to go too and how they tackle the objectives.
As a whole, the best C/O's sit back and take in the entire situation as they have a clear overview of what is happening across the entire battlefield, Squad leaders don't really have this opportunity as their minds are purely set on attacking and defending said flags and they rarely have time to assess the movement of other squads.
The C/O's main responsibility is to keep the team notified of enemy movement and inform the Squad leaders of any other relevant information the help them with their objectives.
Let me put this into a simple scenario;
Having Captured objective Bravo, the team has rushed ahead and started capping objective Charlie. Unfortunately, in the rush, objective Bravo has been left defenceless.
Unknown to the rest of the team, objective Bravo is slowly recaptured by the enemy. Luckily, the C/O has utilised the UAV and has noticed the mass of enemy infantry sitting at Bravo.
The C/O can now do the following-
1) Instruct each individual squad on where to go, trying to micro-manage the situation.
2) Advise the team of the mistake and ask for a squad(s) to volunteer in defending Bravo. Possibly request an Area attack to see if the stops the capture of Bravo.
Choice 1 - As stated in previous posts above, its very difficult to instruct players on which flag to go to. Don't know if this is due to ignorance or human nature but people generally don't like being told exactly what to do! Every squad leader has a different approach to how they want to play a map, the C/O shouldn't really restrict how they do this.
Choice 2 - Asking for volunteers, from my experience, tends to be the better approach as you are not technically instructing them on what to do but merely advising them of a better approach. If the C/O manages to get a squad to fall back, great! However, If there is no response, its not a disaster. In the end the C/O has done his job.
A C/O has also many tools available to them the help assist the team, such as:
Area Attack - Clears out groups of enemy's on the map, great for assisting with a big push or defence.
UAV - Recon, greatly improves the teams ability to assess the entire battlefield.
C/O Rally - You can get your boots on the ground and assess the situation on the field. Helps with morale and a quick rally can assist with a push on a difficult objective.
In general, a C/O shouldn't act as a micro-manager but more as, you guessed it, an adviser to the team.
Finally, it helps being a "recognised" player on the server when acting as a C/O, but this shouldn't stop less experienced and known players from taking up the role.