If you're playing a large game it's helpful to understand what the force organisation charts represent. Basically the charts allow you to organise a force based on a military formation called a detachment. A detachment is a collection of units that move and fight together on the battlefield, and is the smallest formation that can be used to carry out a mission. During a campaign all the units in an army will be organised into detachments, and will tend to carry on operating in the same detachments throughout the campaign.
For example, a Space Marine company consists of over 100 Space Marines split into 10 squads, backed up by a large number of ancillary vehicles like Rhinos, Land Raiders, Predators and land speeders. Using the company as a single force would create a huge and unwieldy formation, while ordering the squads and vehicles around on their own would be a nightmare for the company commander. Because of this, at the start of a campaign each company will be split into two or more detachments, and it is these that will be used to perform all the duties that the company is called upon to perform.
Carrying on the example above, if the Space Marines were called upon to carry out a mission they might assign a single detachment to carry it out. This would be the equivalent of playing a small game of up to about 1,500-2,000 points. For a larger mission the company might assign two or more of their detachments. This would be the equivalent of playing a higher points value game with each player being allowed to field two or more 'armies' in the same game.
So if you're playing a very big game of more than 2,000 points a side you can simply field two or more 'armies' on each side, with a separate organisation chart for each army. This is especially useful for very numerous armies like Imperial Guard or Orks which will struggle to field enough units to use all their points using a single force organisation chart.
Alternatively, you could simply double up the number of boxes available on the force organisation chart for each side, or mutually agree to increase them by a set number. There should usually be a ratio of two to three Troops boxes to each extra HQ, Elites, Fast Attack and Heavy Support box. If you want to get really wacky you could even roll for each category, adding D6-3 boxes, or a D3 to each one.