Highlight is a common method of Bible mark up for good reason. It's easy to do and makes sections clearly stand out.

Pros

• Simple
• Can be used with a color scheme.

Cons

• Little context (why did you highlight this part?)
• You can't overlap highlighting.

Underlining is similar to highlighting but you can cross underlined sections over. It also uses standard pens, not highlighters

Pros

• Simple
• Can be used with a color scheme.
• Can overlap
• Uses common pens

Cons

• Little context (why did you highlight this part?)
• Can be difficult to distinguish
• Can look messy
• You may need a ruler to keep lines straight

Instead of underlining, create a box around the section. This helps distinguish and can be overlapped. It's more forgiving on squiggles.

Pros

• Simple
• Can be used with a color scheme.
• Can overlap
• Uses common pens

Cons

• Little context (why did you mark this part?)
• Can be harder to notice

If your Bible has space, you can write notes in the margin connected to the passage you are reading.

Pros

• Detailed
• Can be used with a color scheme.
• Adds extra information
• Easier for future self to understand

Cons

• Requires wide margins or small handwriting
• Can be difficult to connect not to passage

Instead of writing your notes next to the scripture, you write a reference to where your full notes are. This requires a second notebook.

Pros

• Works with all wide and narrow margins
• Allows for very long notes
• Can be cross referenced in other notebook

Cons

• Little context (what does this number mean?)
• Needs another notebook
• Storage and finding can be tricky

You don't have to pick one method, you can combine two or more to get the benefits of each. My personal approach is the box method with miscallenies but I make use of occasional margin notes and highlights too.

Find a system that works for you.