Under most circumtances if the transfer is successful the PLC should function properly. When you do communication under windows there tends to be more communication error, but the built-in error detection take cares of it most of the time. However, it is not 100% fool proof that's why we advise you to start in pure DOS mode. (Even for WinMe, you can start into DOS mode using the startup disk).
Sequencer is very useful tokeep track of the "State" of a sequence of actions (heard of "State Machine"?). Think of your washing machine, at different part of the wash cycle different things are activated and a sequencer can be used to keep track of each step of the cycle very easily. Sequencer need not proceed one step every fixed period. It can be triggered by events or timer or both. You can even use the [StepN] function to jump to another step asynchronously. Implementing it in ladder logic can be pretty challenging.
Latch relay holds its state once activated and need to be cleared by the [CLEAR] function. Internel relays are just memory bit used to remember an event. They are commonly called a flag.