If I'm drafting a team where the AL will have the DH and the NL won't, how does realignment work?
I mean if I draft my team for the NL and get put in the AL... well, you get my meaning.
How can I be sure I draft the way I wish?

You can draft however you want. Its the commishioners job to manually realign the league said way.

Yeah, I'm not a fan of this either.  Half of the teams will have a man on the bench that could/should be starting if they draft assuming your gonna get a dh.  I know some people like it but i'm just not one of them.

Ideally the commish will allow you to specify ahead of time if you're playing in the AL so you can draft accordingly - if you do that it is a perfectly valid setup. If the commish forces people to guess, well that's just dumb.

yeah thats what happened w a league i'm currently in.  

meaning he didn't tell us who was going to be in NL and who was in the AL.  

There was some reasoning behind my madness for setting the league up with DH in the AL and not in the NL.  First of all, we're playing with a cap of $140 million, so paying for a DH that will sometimes sit on the bench really isn't that big of a deal when it comes to setting your roster.  In this game, $140 mil is a lot to play with and everyone in the league is playing under the same rules.  We are also playing interleague, so the DH will get used even if you are in the NL.  It also gives you an extra pinch hitter...and the fun factor of finding a solid utility player with some PA that you can use to rest other players.

Sorry if it was too mind numbing for you to strategize.  I know that the real teams in MLB have to deal with the same exact rules since the advent of interleague play.  Nobody pointed a gun to your head to join the league...and yet...you placed 2 teams in the league.  In fact, I dare say you like my leagues. I've only created 2 leagues of 12 teams each and you've placed 3 teams in those 2 leagues.  So I thank you for your support.  :-)

If I don't like the looks of a league, I won't join it.  If I doubt the competence of the commissioner, then I won't join the league.  And if I whine so much that someone calls me names, then I accept it and move on (although I tend not to whine too much...especially over minor things...I do like to question and find answers though especially in a fun game that I have yet to figure out).  And if someone calls me a name or two, I don't obsess over it. LOL  Not everyone in this world is going to like you and that is okay. 

If I join a league, I don't ask the commissioner to change the league format just to benefit the way I want to play.  That seems odd to me.  Why not just create your own league?  Or join a league that does fit what you are looking for...oh wait, perhaps you find the competition so very easy for you to win in my particular league because it is basically a group of  buddies that have gotten together to play but didn't have enough people to fill all 12 slots so the league was opened to new friends too.  Sounds like someone didn't get exactly what they HOPED for and then whined about it to the world. 

So was the alignment truly random or did your buddies know where they'd be? I don't know the specifics of the theme but normally in a 140mil league I could spend the whole thing without a dh, so I'd want to know.

Just because a few people are willing to live with the setup doesn't make it correct, and i think most sim players would agree that it's wrong.

Now if you advertise that it's just luck of the draw and enough people are into the challenge to fill the league, that's cool. No one says theme leagues need to follow what most people would want.

wow I wasn't even talking about his league and he comes out swinging haha.  

Are you guys married?  

I wish, he treats me better then my GF...

By GF, epolice means his left hand. LOL!!!!  The guy is obsessed with me.  Look at all these posts on the forum. Hilarious. JFRANC - League was random.  Sticky fingers asked me to change the rules to the league before he joined and I didn't.  He wanted me to do this and that and I didn't. So he got all pissy about it like a little girl who lost her favorite barrette.  NOBODY else in the league is complaining.  It's a fun league and sticky fingers is making it even more hilarious with his idiotic comments nearly every day. LOL  If the guy doesn't get  what he wants, he cries and fusses and hoos and haws, and...you get the drift.  Here comes a ton of more comments...wait for it...wait for it....here they come.  LOL