I usually try to avoid attacking the deck, but once in awhile I have to in order to attach it. :-)
Some kits have decks that fit better than others. I've never had
trouble with Tamiya decks, but had a tough time with the North
Carolina's deck on the Trumpeter kit.
What kit are you specifically having problems with? Chances are I've built (probably more than once) and can offer some advice.
Basic advice is to fit the deck prior to gluing it. I'd also recommend
using a welding agent like Tenax or ProWeld. Typically, I start at the
bow, fit the deck piece, and apply a bead of ProWeld to the seam using
a Touch-n-Flow applicator. This also gives time to make an minor
adjustments as I go. Once that's set, I'll add the center section of
the deck and repeat the process, paying more attention to the deck
joint across the beam instead of along the deckedge. The deckedge seams
are far easier to clean up than across the planked deck. After fitting
the rear deck section, I'll focus on the seam at the joint instead of
the fantail, again, it's easier to address those than the deck joints.
The key is to test-fit everything at least twice before you apply glue,
and to start at one end of the ship and work your way aft, or forward.
I also can't stress how much easier it is when you're using a
Touch-n-flow with a welding agent.
Jeff