if a PC buys mods during character creation... Should they be auto-equipped, or he needs to roll for it during a session.

Also, economy is not my strong suit... Our group is going to start a campaign owing money to a hutt, as an obligation, how much money should they owe?

Attachments can be purchased freely and applied to gear. Mods can be purchased, but someone will still need to apply them in-game through Mechanics checks. As always, these can be failures resulting in the credits spent on the Mod going to waste.

Page 310 has an example of paying off a debt that has 50,000 for 10 Obligation but, to be honest, it doesn't really matter. What's more important is that whatever value you set it at, you should ensure that it's difficult for the PC to pay it off. You can do that either by making the obligation large or just by having their job rewards be more tangible things, like weapons, ship mods, or services/favours.

I would recommend that you instead have a discussion with your player to figure out why they have that debt. That should give you a better place to start.

Also, economy is not my strong suit... Our group is going to start a campaign owing money to a hutt, as an obligation, how much money should they owe?

A nice angle is to start them out with a ship (the CRB gives some examples) and then assign the players the cost of the ship as debt they owe to some patron. It'll be a nice big number plus interest which guarantees the Hutts, or Black Sun, or whoever will be a shadow over their path for adventures to come.

At character creation, especially if it's not a beginner character I usually allow mods, but the installation cost must be paid extra.

Using Han Solo's as a basis then multiply the obligation by a 1000 but it really depends on what replaces that obligation if they manage to pay it off.

The above response sounds a better way to handle it but how much input do your players have on the game you intend to run?

On questions of economy, things are very relative. The biggest thing is to balance pacing between how much they owe and how much you're paying them for each job. Near the back of Dangerous Covenants is a table for payouts for merc jobs, and could be used to roughly approximate how quickly your crew should be acquiring credits. Then figure out if you want the Obligation to be around for a long time, or to be almost paid off (after all, the debt might not have been made yesterday, and payments may already have been made).

Also, remember that just because the debt is technically monetary, doesn't mean that the payoff always is. Favors, extra goodies, or even saving the Hutt's life from an assassin or a hostile takeover, all can play into reducing the Obligation.

TL;DR: Figure out how you want the Obligation to impact the plot (with your players input), then adjust the numbers to fit.