Good DATA Practices: SQLite vs Excel

So I'm essentially trying to understand the best way to approach data (in Python) but don't know where to start researching as I don't exactly know the terminology to find information about what I am trying to do.

My main point of concern is how I should work between SQLite and Excel.

The reason I say this is I have 100's of standardized excel files that are constantly having rows and columns added to them but am not sure how I should approach reading and manipulating the data i.e. should I leave it all in Excel (where cell ID's are changing) or should I be working within SQL as it is a relational dataset in which I don't need to know the specific locations of the cells I want to read and manipulate.

Any general comments on resources/best practices/tutorials would be appreciated.

Thanks in advance