The Inertia Problem
Its always been known that inertia is going to squish you flat if you accelerate or decelerate to quickly. The problem is actually solved using the same technology used to fold space and create compressions.
String Manipulation Fields.
With the case of the String folding drives (Compression Drives) the drive manipulates several strings at a time and uses those fold space. The strings are of a specific size on which are large enough to actually accomplish a spatial compression. Since we know that Gravity and Magnetism are actually just string manipulation of varying degrees, Inertia was overcome by using a level of string manipulation which essentially freezes or binds local strings of a type. IN this case, a String Manipulation Field (SMF) is used to avoid inertia altogether since the strings used for FTL are much much larger than the strings which a ship and its internal contents, people equipment, etc use.
This is also the same method to generate artificial gravity. Since SMF's are localized, several can be generated at once achieving several effects at the same time.
A secondary system called Inertial Compensator's are also employed, but are using energy redirection instead, like a spring. The energy caused by acceleration and deceleration are transfered using less complex string manipulation, but isn't field based, and are tuned for each ships string signature. This causes a minor indirect SMF reducing the forces of inertia directly on the ship and its occupants.