What's the best way to approach
As a general rule, you generally connect through hole components with tracks on the bottom layer. The reason for this is:
1/ It leaves more room on the top layer for connecting the SMD components (remember it is always better to reduce the number of vias wherever possible) and;
2/ You are less likely to break/damage the tracks when removing through hole components when repairs are necessary.
Many people starting out, think they will actually save money by designing boards that utilise only one layer. This *may* be true with punched boards, but it generally not true with etched boards. The board shop will use 2 sided copper board & will completely etch away the unwanted layer. This puts copper into solution which must be removed before the waste liquid is disposed of. This costs money.