I'm confused... are you asking how you query this? How you do the logic for this? The query is straight forward, a select and insert works just fine.
Also, its not good to have multiple columns for the same datatype. In the future, if you want to expand to 6 skills, you have to add 6 columns, edit a bunch of code, its messy.
Instead, you can create a mapping table like so:
The skillNum is only there in case you care which skill is first, second, third. You can drop this if it doesn't matter.
CREATE TABLE skillMap(
user_id int not null,
skill_id int not null,
skillNum int not null,
primary key (user_id, skill_id)
This way, if you want a user's skills, all you have to do is join skill on skillMap where user_id = something. And in the future, if you decide to drop to 2 skills or go up to 20, no (or nominal) changes are necessary.