Hi,
This is nothing unusual. it all depends on your payroll setup - eg if it's setup as monthly rather than hourly pay, this is normal. It could be many places you need to change and would take at least a few hundred pages to explain here.
From the way you ask your question including the subject line: am I right to assume your are not talking about a life system, but a sandbox you are playing in and you just got started with HR without any training so far?
This is not, where this forum can help. You are supposed to use the basic dicumentation and training available first. Your question is so fundamental that it's no different from "can you explain SAP payroll".
Please refer to the available training and doco on help.sap.com and wikis here on SCN.
For your current sandbox play: try to capture an absence with an unpaid absence type for the two days the employee is away and watch what happens.