I'm sure there are specific strategies relating to pipe flanges, but for the broader issue of controlling that all of your bolts are tight enough, here is some background information.
When tightening bolts in any clamping application, what's really important is the total clamping force. In any simple joint, and specifically when dealing with pipe flanges, the clamping force in the joint is the same thing as the tension in the bolt (also known as preload.) Torque is sometimes used as a surrogate for preload since the two are correlated, but for a number of reasons, it is not a very good tool for measuring clamping force.
The relationship between torque and preload is based on some things that are fairly easy to quantify like the thread pitch of the thread, but also on things that are hard to quantify like the accuracy of the threadform, the quality of the coating, the cleanliness of the fasteners, etc. The amount of torque that is translated into tension is a relatively small percentage of the overall torque, with the remainder overcoming friction, often quoted as 10%. Because many of these factors are hard to quantify and hard to control without very detailed quality control, torque does not always offer an acceptably accurate way of predicting preload. (More on the torque-tension relationship: 1 2 3)
To overcome this problem, when the amount of preload is critical, we measure the tension in the fastener directly to calibrate our tightening system. One way to do this is with a device colloquially known by it's brand name, Skidmore-Wilhelm. A bolt can be tightened around this device, and the tension is measured. In structural applications in the US, per the RCSC (PDF Warning) it would be typical to tighten 3 bolts out of each batch against the machine, using either a torque wrench, or by turning the nut a certain number of degrees past 'snug-tight.' If those 3 bolts fall into the acceptable tension range, then that torque or angle is used to tighten the actual production bolts until that batch of bolts runs out, or the next day, when the calibration procedure is performed again. Torque or angle are still being used as surrogates for pretension, but they are being calibrated for all of the unknown variables regularly.
More recently, some methods for measuring the tension directly have emerged that are affordable enough that they can be permanently used for each bolt (whereas the Skidmore-Wilhelm costs thousands of dollars.) These include bolts with heads that change color when preloaded, washers that squirt out paint when preloaded, and bolts with a splined end that breaks off when preloaded. These methods are generally considered to be more reliable than conventional bolting by calibrated torque or turn-of-the-nut (the method that uses angles) but do increase materials costs, so they may or may not be appropriate for your application.
