After each executed 68000 instruction, QLAY will check whether there is internal housekeeping to be done. This is when exceptions, interrupts, and timing events like the 1msec tick are handled. QLAY will then proceed with the next instruction according current value in program counter. QLAY does not patch any ROMs and does not access any of the QDOS system variables directly. Emulation speed depends on many factors.
Higher number is faster.
The tools are needed because the QL and it's operating system QDOS have some pecularities that do not match well with most other Operating Systems. To allow transparent access from the emulator program to the native file system it's needed that the file header is stored separately. It knows about datasize fields. And will import and export files from other QDOS compatible systems and QLAY's MDV file format. The files can then be used in QLAY directly.