Many things affect the accuracy of the Magellan II as installed on the LX50.
Accurate leveling of the tripod.
This is extremely important! I have looked at two Super Wedges and have found the bubble level in the top to be inaccurate as well as hard to use. I purchased a larger bubble level from the hardware store and installed it in the following manner. The larger level is much more accurate. The stock bubble can be readjusted by carefully prying it out and re gluing it in the manner described below.
1) Remove the wedge from the tripod.
2) Carefully level the tripod using a known good level. Measure the level in three directions for accuracy. Extra effort here pays off in the field!
3) Very carefully mount the wedge and tighten the three Allen bolts used for the azimuth lock.
4) Trim the housing of the bubble level (if needed) to fit into the area selected. Clean the back of the level and the area of the wedge where the level will be adhered with rubbing alcohol.
5) Using black RTV sealant mount the level on a 1/8" to 3/16" thick puddle. "Adjust" the bubble level to get it level. You may have to tape the level to get it to remain in adjustment until the sealant cures. The sealant should cure enough for the level to stay put in about 3 hours depending on temperature, material used and humidity. Check back from time to time over a 4 hour period to make sure the level does not slip out of adjustment. A faster and easier, albeit more permanent, method is to use 5 minute epoxy. This is the manner that I attached mine.
The level can be replaced by scraping it free with a stiff dull knife. A brass bristle brush will remove remaining sealant from the wedge and level allowing reinstallation if needed.
(Click to enlarge)
Polar alignment
The accuracy of the polar alignment has much to do with the Magellan's pointing accuracy. I use the following method to align my wedge.
1) Plant the tripod and wedge as close to pointing north as is possible.
2) Level it as carefully as possible!
3) Adjust the angle of the wedge using an inclinometer or a digital level. The digital level I think is the preferred choice for several reasons, it is highly accurate (0.1 degree) is easier to see by light of flashlight and you can convince your wife/girlfriend that things around the house will be level/plumb and much better looking when you get one. I use a GPS coordinate (it's up to you to figure out how to convince your wife/girlfriend that you have to have one) to set the latitude, I have never had to re tweak the latitude using the GPS and the digital level. The picture below shows both types of devices. The digital level costs around $100 and is 24" long, the inclinometer should be under $25
4) Drift align the azimuth of the wedge. There are many descriptions on how to do this on the web, here's the Beevo short 'n' sweet version.
a) Point the scope at a star near the meridian as close to 0 degrees on the DEC circle as possible.
b) Center the star in a reticule eyepiece. With the scope powered up watch which way the star drifts in the crosshairs. You are interested only in UP or DOWN movement.
c) If the star move UP turn the Azimuth adjustment so the star move RIGHT in the field of view (I am assuming you are using a star diagonal) Repeat until the star does not drift UP or DOWN.
If the latitude of the wedge was set accurately with the digital level no further adjustments should be needed for visual and light duty photographic use.
(click to enlarge)
Magellan II Electronic alignment
The next thing to look at is the Electronic Alignment (alignment) of the Magellan II. As pointed out on several web sites the Magellan can be aligned using a "One Star" method. I actually have found this to be the easiest and most accurate. According to Mike Leigh, the guru on the Magellan II and LX50 who alas is no longer with MEADE, a score of anything other than 100 on the alignment will not yield good GO-TO results. BTW, I like to think of the Magellan II as a GO-NEAR system! :o) If the Magellan puts the object dead center in the FOV every single time, what fun can you have finding things, right?
1) Set the OTA to 90 degrees (I use the digital level across the corrector housing) See the Setting declination setting circle page full details on how I use the level to adjust the DEC circles.
2) Turn on the scope and select ALIGN.
3) Follow the instructions until you have synced on the first star (choose a star in the area you are going to start your observations).
4) Every time you locate an object that is in the database of the Magellan sync on it. Select the object from the database so it is displayed on the screen, hold the ENTER button down for 1 second, center the object carefully and then press the ENTER button again with a short push.
5) If you move to another area of the sky select a nearby star that is in the Magellan's Star list (available on the download page) and sync on it first. this procedure makes the Magellan more accurate as the night goes on irregardless of the alignment method you choose.
OTA Alignment
Instead of typing my little heart out I am going to provide some links on the OTA alignment.
Meade Control Panel and Motor
Information 
The source quoted is Mike Leigh from Meade. He was the man, and long since gone!
the
LX50 comes with two motor/chip sets. An RA motor assembly stamped 500K (the
older ones) should have a thinner chip labels version 3.1. A motor assembly
stamped 1K has a chip labeled 5.3.
.Mike says that some had had problems
due to chips and motor assemblies being mismatched. The correct (newer) chip
would have a sticker on it that reads 35-4000-12R5.
Page updated 9/1/06