They do not interact at all.
The wielder may use the tools to create items using the Craft skill much more surely and quickly.
The tools are used to make mundane masterwork-quality items. While when creating magic items, the mundane object should be present before you start the process.
It then follows to explain the differences and bonuses granted by the item:
The wielder may take raw materials with a value equal to half the price of an object to be crafted, and produce a finished object in as little as 1 hour for an item with a final cost of 2,000 gp or less. For objects with a final cost of more than 2,000 gp, the wielder can perform 2,000 gp worth of work in a single hour, but only once each day. Only a single skill check is required to successfully complete the item, made on the last day of crafting and gaining the +4 circumstance bonus granted by the tools.
- The requirement of 30% of the item's cost as raw materials is replaced by 50% of the item's cost.
- The time spent on the process is much shorter, hours instead of weeks.
- You only make a single skill check instead of several skills checks per process period.
Although the Magic Item Creation rules say that you can use another skill other than Spellcraft, the method of crafting being used is not the Craft skill.
At the end of this process, the spellcaster must make a single skill check (usually Spellcraft, but sometimes another skill) to finish the item. If an item type has multiple possible skills, you choose which skill to make the check with.
That means that if you do everything by yourself, the process is much shorter, as creating masterwork quality items usually take much longer than enchanting with magic.
For instance, crafting a masterwork (+150 gp) full plate armor (1,500 gp) should take over 10 months for a single character with about +10 on his craft skill, as seen on this calculator. The tools make this possible in less than a day.
You do receive the tool bonuses for using the Craft skill to create magical items though. That is the point of being able to use a different skill other than Spellcraft.