You will want to use an automatic continuous/servo mode to photograph birds in flight (BIF). Most modern cameras support some kind of servo mode, even entry-level cameras. Using servo mode is only part of the solution to tracking BIF, however. More advanced cameras offer additional AF features, such as multipoint AF Expansion or Zone AF that will use more than one focus point around your key selected point. The use of an AF Expansion/Zone AF mode will improve your tracking ability over the use of a single point. Tracking ability is often dependent on the AF system used, and if you have the option, using a system with more and denser points, particularly those with configurable zones, will improve your ability to track subjects.
Additionally, a denser AF system, such as the newer reticular 51-pt Nikon and 61-pt Canon, offer more points that are more closely spaced together which can greatly assist in subject lock and continuous tracking. Most Canon cameras have a 9-pt AF system that is not reticular, and there is quite a bit of space between each point. The Canon 7D uses a 19-pt AF system that is not reticular, but definitely denser than the standard 9-pt system, and every point is a high precision cross-type point which can identify and lock subjects much more quickly. Canon's 19-pt AF system supports Expansion and Zone AF modes. Canon's newest AF system is their 61-pt AF system with 41 cross-type points in a reticular design. This AF system is currently only found on the 1D X and 5D III bodies, however it is the most advanced AF system available at the current time. It supports full multi-dimensional tracking (frame position, distance, RGB color information), multiple types of zone and expansion AF modes, as well as spot AF (smaller area single-point AF, which can be useful for focusing on very precise locations...say a birds eye). Canon's 61pt system is also the first to offer 5 center double-cross type AF points with ultra high precision for extremely fast focusing.
In Nikon systems, there are 11-pt and 39-pt AF systems in lower-end bodies. The 11-pt systems are roughly similar to Canon 9-pt systems, however their 39-pt system is more of a reticular design. It offers 9 cross-type high precision points around the center. All Nikon AF systems support what they call "3D Tracking", which simply means they use frame position, distance, and color information to help inform the AF system of where the subject is likely to be in the next frame, supporting advanced tracking. To use 3D tracking, you must use all 39 points, which is actually less effective than it may sound (more in a bit). Nikon's latest AF system is their new 51-pt, which is also a reticular design. It supports some semblance of Zone AF, although it only works around the center point. The strength of Nikon's system is multi-point f/8 AF...up to 11 points with a single center cross type and 10 surrounding line sensors. This can be a bonus if you intend to use lenses with teleconverters that reduce the maximum aperture to f/8 (i.e. a 600mm f/4 lens with a 2x TC for 1200mm.)
If you intend to track birds in flight, your main options are going to be multi-point mode (all points) with dynamic subject tracking. This would be all 9, 19, or 61 points in a Canon body, or all 11, 39, or 51 points in a Nikon body. This is often recommended by each brand, however it is not as effective or guaranteed as it sounds. When using every single AF point, the camera...rather than you, decides which points should be in focus. Its not uncommon for an AF system, even an advanced one, to decide it should focus on something other than your subject, suddenly switching subjects without warning. Additional tracking logic can be used when performing multi-point dynamic AF, and when used right, it can be very accurate...but you will always have that potential for instantaneous subject switching hanging over your head...and when it strikes, you can lose that keeper moment.
In the area of configurable AF tracking for birds, I think Canon has the general edge. Their new Zone and Expansion AF modes allow you to select the AF point you wish to be your key point, and configure how many points around that key point can be used to continue tracking if your subject moves beyond the range of your key point. Expansion mode simply selects the four adjacent points, top/bottom/left/right, and marks them active but secondary in "spot AF" mode. If your subject moves away from your selected point and onto one of these four neighboring points, it will continue to track. Zone AF mode is similar, however if will use as many neighboring points as possible, all as full AF points (vs. spot AF points). In the 7D, Zone AF can use up to 9 points at a time, and in the new 61pt AF system you can configure how large the zone is. Tracking birds in flight with Zone and Expansion AF around ANY point is the best way to go, if you have the option. Currently, it is only available on three bodies, the 7D, 5D III, and 1D X.
Nikon offers similar functionality, however I believe it only works around the center point. Nikon's zones extend a strip of line sensors out nearly to the edge of the AF spread range, which helps you continue tracking subjects as they move across the frame. This is a small limitation over the Canon system, but it can still be used effectively. If you have supertelephoto lenses and teleconverters, you can use up to 15 points with lenses that have less than f/8 apertures (such as an f/4 lens with a 1.7x TC), or 11 points with lenses that are f/8 apertures (such as an f/4 lens with a 2x TC or an f/5.6 lens with a 1.4x TC). Some of these points remain cross-type as well, offering high precision, low light, multi-point AF ability, something not currently available on any Canon body.
Finally, you will probably also want to configure your AF system a bit as well. You will want to prioritize AF acquisition and tracking over AF drive and shutter release. This will prevent you from being able to actually start taking pictures until the AF system has a lock on your subject and is able to track. You will also want to support continuous tracking, and avoid shutting off the AF system when it determines the subject has moved beyond the edge of the frame. Finally, you will want to tune the AF system to switch subjects slowly, rather than quickly. A moderate slow setting will be good for most birds, including those with erratic flight. If you are photographing when multiple birds are in flight, using the slowest tracking sensitivity, as that will limit how often the AF system decides to switch from one subject to another when they cross paths in your viewfinder.