If the recordings you are making with MixPad are not perfectly synchronized with each other, then you may have hardware latency issues. You can specify an offset in milliseconds in the program which will automatically adjust your recordings.This option is only available if you are using an MME recorder. The issue of latency should not affect you if you are using an ASIO capable sound device and selecting the ASIO drivers for both playback and recording.
To set the offset recording you may go to MixPad > Options > General > Audio recording.