As you are likely to know, every time you level someone up using Bonus Experience, three of their stats will increase. However, it is better to save your Bonus Exp for a character's later levels, when they have maxed out some of their stats. This way, when you use it on them, stats that they normally wouldn't gain much increases in will suddenly start skyrocketing.
For example, Micaiah is almost certainly going to max out her stats in Magic, Resistance and Luck (if Light Sage) very quickly, but lacks in some of the other stats, most significantly Speed, as she's usually too slow to double attack most enemies. However, when her Magic, Resistance and Luck are maxed out, start using Bonus Experience and watch her Speed rise.
When you use stat increasing items (Talismans, Secret Books etc), be sure to use them on a stat that a unit is lacking in. For example, using a Talisman on Ike will increase his Resistance, which is one stat he's lacking in. However, increasing his Strength would be a waste of time, as he's likely to max out his Strength stat by naturally levelling up.
When a unit is at level 20, you can use a Master Seal (if they are going to level up to second class) or Master Crown (if they are going to level up to third class) to have them change classes instead of using Experience. Since they are at level 20, you won't be missing out on any stat increases anyway.