I've used bottle jacks as well, but I might suggest a regular hydraulic floor jack - the kind with (4) wheels and a long handle. These aren't expensive, either (although a little more than a bottle jack) but they are MUCH more stable. The contact point is about 4-times as big and the base is many, many times larger. Now, since you don't need to remove the boat, here's what you do:
-- Loosen the bow strap a few inches
-- Crank the tongue jack all the way UP
-- Place the jack under the keel at the stern of the boat
-- Jack the boat up until the aft end of the boat is a just a few inches off the bunks (rollers?)
-- Now you can physically push (this is ESPECIALLY where a floor jack is better suited) the boat to make it lean one way or the other to facilitate working on one side or the other
-- Once you have the boat leaning the way you want, you can tie a rope from a mid-ship cleat (on the low side of the boat) to the trailer frame. You can also put some blocking between the trailer frame (like a 2x4 with the ends notched) and the high side of the boat. You won't need much - they usually pretty much stay by themselves, but better safe than sorry.
Without a floor jack, or any type of jack:
-- Start with the tongue jack all the way DOWN
-- Use concrete blocks (set in pairs, and alternate their orientation) to build cribbing to get you close to the keel. Finish with one block.
-- Now finish with wood (2x4's and/or 4x4's, etc). Be sure to lay the final piece of wood with the grain perpendicular to the keel
-- Now simply raise the tongue jack till the keel again is a few inches off the trailer
-- Finish the same way as above.
If you want to lift the whole boat off the trailer we can do that, too (w/o removing the trailer). We can do that with just a floor jack, as well. Sometimes you can even do it with just the "tongue jack" method I mentioned above. You'll need somewhere between 11 and 17 blocks, depending on how high your boat sits off the ground while on the trailer. You can estimate by measuring. If you want to do this method, let me know. But it's similar to the second method that is mentioned by Jbrinch.