In series
Modern vehicles with OBDII based PCM's and Can Bus systems can be a
challenge to tune effectively when the vehicle has been modified.
We wanted our customers to have an enhanced driving experience as often
as possible so the iEMS3 (integrated Engine Management System) was designed
to produce gains across the entire RPM band, unlike other tuning solutions
which simply modify the Wide Open Throttle range (WOT). Producing a
higher RWHP & RWTQ number at 5500 RPM was not our goal as that RPM
is rarely used. Simply inserting a pre-programmed Smart Card immediately
changes the program settings for the current driving situation or octane
of fuel
System Overview:

The BC system allows precise tuning of the air to fuel ratio and ignition
timing over the entire operating range of the engine. Simply inserting
a pre-programmed memory card immediately changes the program settings
for the current driving situation or octane of fuel as desired. The
unit contains its own fuel injector drivers and is wired in between
the factory PCM and engine. It is especially useful for recalibration
of both forced induction engines and those with extensive modifications,
allowing the tuner to quickly get the engine running correctly. Stock
engines can also benefit greatly from improving the fuel curves.
The BC-system is similar to a stand-alone engine management system,
but also has similarities to current "piggyback" systems.
It is actually a heavily modified Stand Alone Engine Management System
that has been modified to work in conjunction with a factory PCM. We
consider it as working "In Series" with the factory PCM, basically
a supplemental fuel and timing computer system.
In a true stand-alone system, you must program for every operating condition
the engine will experience, such as load, throttle position, RPM, engine
temperature, air temperature, etc. These systems can be quite complex
to tune. Most PCM’s also control radiator fan operation, A/C operation,
emissions operation and diagnostic functions.
Stand-alones are generally not compatible with OBD2 emissions testing
in that they replace the factory PCM and will not link up with state
run emissions equipment. Nor will they allow functionality of the remainder
of the modern Can Bus system. These systems are best suited for racetrack
use where engine tuners can fine-tune the program to the environment
of the moment for optimal performance. 
In the current "piggyback" systems, control over the engine
is done by manipulating inputs to the stock PCM. Manifold air pressure
and oxygen sensor voltages can be altered in order to make the PCM change
its load calibration, thus altering fuel and ignition advance curves.
Reducing MAP sensor voltage has the effect of reducing injector pulse
width by making the PCM "think" the engine is under greater
vacuum than actual. This is MAP sensor voltage skewing in a crude and
somewhat unreliable method of fuel control.
However, at the same time, ignition timing is advanced due to the PCM
believing the engine is under a lower load. Conversely, increasing voltage
has the opposite effect, increasing fuel and reducing timing advance.
When tuning with systems of this type, you find yourself in situations
where you can have proper part throttle tuning, or proper full throttle
tuning, but rarely both if the engine is heavily modified or has forced
induction. To make matters worse, today’s vehicles are too smart
for such methods, and will simply readjust for any input that is a constant
or repeatable input. This very quickly erases any changes that are attempted.
The current PCM file rewriting software that is on the market, works
well on NA engines. However, due to limitations in the physical architecture
of a Modern PCM, it is impossible to tune for all operating parameters
when adding forced induction. This is due to the fact that a factory
NA PCM just does not have the capability to be properly adjusted for
a pressurized manifold state of operation. The only way to increase
fuel during boost is to simply lower the WOT threshold which is generally
a function of throttle blade opening percentage. 
This has the effect of basically telling the PCM that the car is in
a wide open throttle state when the drivers pedal position is no where
near a similar position. When this occurs, the car simply wants to go
right now, and lunges ahead. This makes it very difficult to operate
when under light load situations, such as moderate acceleration, merging,
shallow hills, etc. The effective travel range of the accelerator pedal
has been greatly reduced. This can cause additional difficulties such
as decreased gas mileage since the vehicle is running in an open loop
mode with very rich fuel ratios when it should be in closed loop mode
operation.
Since the factory PCM can not be written to actually understand boost,
there will always be a window (in particular with a turbocharger) where
the vehicle can be developing boost (part throttle boost), yet there
is no fuel correction. Conversely, in trying to lower the WOT threshold
as described above, you can wind up with extreme drivability issues,
and it’s just not a fun vehicle to drive. To make matters worse,
generally a 2 Bar or 3 Bar MAP sensor is added to prevent overanging
the voltage signal sent to the PCM. This can have the effect of telling
the PCM that the vehicle is seeing a much lower load than it really
is, and can result in lowered transmission line pressures when you need
it most. This is similar to the same problems found when using a MAP
sensor voltage skewing "piggyback" system.
The iEMS3 offers the best of both worlds. Stand alone system control,
but with the simplicity of a piggyback system. The iEMS3 controls fuel
and timing, leaving the stock PCM to handle all other functions, such
as idle speed, A/C control, emissions operation, etc.