Easiest issue first: If you are concerned about how something will look because of the color, bring your own sharpies and just politely ask if the band members wouldn't mind using yours because you want it to look a certain way. I mean, if they do indeed have their own in that color already, great. But there is no guarantee, even if that is what they have done in the past. You just never know what the logistics of a particular show are going to be. Just to give you an example, when I was let in to see the band do sound check on the Along For the Ride tour, I was told to get there and go to a certain door at a certain time, call their tour manager, etc. In other words, it was all pre-planned, the logistics were in place, etc. So one would think that everything would have fallen into place and been perfectly organized. But as it turned out, there were a few little snags here and there, including getting let in and the tour manager having to scramble around for the next 15-20 minutes to find laminates for us because they had run out of them in the usual place they should have been stored. Little things like that can happen. If they run out of silver sharpies at the previous show and haven't had time to send someone to buy new ones, or if all the markers get put in the wrong road case and cannot be located by the time of the meet-and-greet, or whatever, the band will just have what they have. Nothing wrong with you being prepared and bringing your own.
As far as what to get signed, that's always a very personal thing. I have gotten standard things like CDs signed. I have also done custom forum tour shirts and gotten those signed, which are a bit more personal. If I were going to have something signed at a show on this leg, I would probably go for a copy of the I&W vinyl, just because it is bigger than a CD and can be framed/displayed if I wanted to do that. But as to whether or not to have Mangini (and Jordan, for that matter) sign something like that, I could go either way. On one hand, he has played all of those songs and is now a part of them, and he is playing them all on this anniversary tour. If you did something like that, I would just tell him something like this before he had a chance to ask you if you wanted him to sign it: "Mike, I know you didn't write or play on the actual album back then. But this is my own personal memento from seeing you play these songs with the band on this anniversary tour, and it would mean a lot to me if you would sign it." I think he would be more than happy to if you did something like that.
If it was me, I'm not sure if I would or not. I mean, I did that very thing with another band in a similar situation in the past. But I could also see just having the members sign it that actually played on it, even if that meant I might never be able to track down KM or Portnoy to get theirs. Hard to say which is the "right" way to go--just think about it in advance and figure out what would mean the most to you, and prepare a short little speech to ask the band and let them know why, like my example above.