have a scratch on my truck that I tried covering up with a paint pen from Nissan which only made it worse (This was years ago before I wised up). You can feel the paint pen and it looks like someone just went over it with a sticky marker. Is there anyway to get this out?
Yes and no... It is possible to wet sand the area to level the high paint spots and then polish that out but I wouldn't suggest that to a beginner. If you wet sand too much you can sand of the clear or you may not be able to polish all of the marks off with the PC either. So not much you could do with it unless you take it to a body shop for a repaint or maybe a pro detailer to try the wet sand.
Also, in terms of a clay bar, it doesnt really seem like theres a favorite, should I just pick up any clay bar and QD?
Any BRAND of clay will work but make sure you don't buy heavy duty clay bar. Don't worry, these bars will be labled so. Optimum, Poorboys, Mothers, Meguiars, Zaino, Pinnacle, Wolfgang, Clay magic are all safe brands to buy.
In terms of wax and sealer, I already purchased the Klasse twins (AIO and Sealant) because it was highly regarded in a Frontier forum (I wish I would have waited since Poorboys seems to be popular).
The Klasse AIO/SG isn't a wax and sealer FYI. The AIO is a paint cleaner and the SG is a sealant. A very good one at that. You;ll have to do some reading on SG to make sure you apply it very thin and do not let it sit on the paint for more than a few minutes unless it'll be a bear to remove. This is actually the two products I purchased when I began and actually still use them to this date.
I have tons of minor scratches on the truck, should I use the Pinnacle XMT line or the Poorboys line?
I use the Poorboy's line. SSR2.5 can take out some heavy swirls and scratches alone. It's one of my favorite polishes. Just make sure you use the proper amount of product (theres a thread on that) and work the product into the paint for a while. It wouldn't hurt getting SSR2.5, 2, and 1 but you might get by without SSR2 if you please.
Also, just to be sure I have the order correct, I am assuming it is car wash, clay bar using a QD as lube, XMT or SSR to remove scratches, then wax and sealant (or sealant and wax?).
Correct. Remember a lot of 'scratches' may not come out...but if they are 'swirls' then you may have better luck. A picture would help. If you were going to use a wax and a sealant, it would be like this: apply sealant and wait 24 hours for it to bond and then apply a carnauba wax. Or you can use one or the other but never wax and then a sealant. Go one step right after the other if you have the energy but read the directions on the sealant for proper drying time.
I also have some 303 for the trim, does it matter when I apply it or should I wait until a specific step?
Do it right after claying/drying. This way if you get any polish that could stain the trim on the trim it would be already protected. It's not necesary but it will help save your butt.
Last question, since I have not purchased the PC yet, is there a specific package one would recommend from Autogeeks suited for my needs?
Any kit would work really. It's all user preference.They are having a sale right now but it ends tomorrow I believe so you may want to hurry

Actually now that I think about it the Poorboy's kit with the PC would work well (
http://autogeek.net/popoprkit.html), because those would be useful in your arsenal or the Edge Kit would be good as well because it offers you everything you need for your PC (
http://autogeek.net/ed20pocacoki.html). Check out DC's store as well for some good deals:
http://www.detailcity.com/dual-action-polishers-accessories.html
Hope this helped... :dcrules