Your comments

According to this site with the update of DSM5 the startup script location has changed to /usr/syno/etc/rc.d

This means that we need to place the Ubooquity start up script in that directory. This command should move the file:
mv /usr/local/etc/rc.d/ubooquity.sh /usr/syno/etc/rc.d/S99ubooquity.sh
Then you will need to tell linux that it can execute this command:
chmod 755 S99ubooquity.sh

reboot
After rebooting check if your ubooquity server is running. After all of that my server should be running, but it isn't. This is frustrating, but in neither start up location was my script being executed... I have the same problem as you.
Hamdan, a post lacking a body is not a post. Next time be more verbose: explain what you mean, give us an idea of what you've tried already and what you think might be able to help.

The only option I can think of is adding the "-Xmx1024m" launch parameter to your command when you launch the Ubooquity jar. This launch parameter will define extra memory for the Ubooquity process. Change "1024" to whatever amount of megabytes you want to dedicate.
After setting up your router to forward port 2202 to your NAS most of you will also have dynamic DNS settings in your routers (if not flash your router with DD-WRT firmware). Make use of those settings by signing up for a noip.com account and plugging those account details in to your router.

With this set up you can sign up for a custom address from noip and use that address to access your comics, via OPDS, from anywhere on the planet!

For example, if you make a noip account and get the address comics.no-ip.org you would put http://comics.no-ip.org:2202 in to your browser. This will connect you to your NAS and display Ubooquity's web interface!

Set up a nice Ubooquity web server and share your collection with your family and friends by giving them your noip address.
Michael, how are you starting the ubooquity.jar file? Are you making sure to add the -webadmin and -port flags? If so what happens after you start the jar and plug the IP address of your server in to a browser window with the port you specified? If you still can't access the server start it without the "> nohup.out 2>&1&" part and read the output Ubooquity prints to the screen. Does it say something about starting the web server?
The -Duser.dir option successfully moved the working directory to a new location. Ubooquity is saving its database and cached files in the new directory. Thanks, Tom!
nohup java -Duser.dir='/volume1/Comics/Ubooquity' -jar -Xmx1024m /var/packages/Ubooquity/Ubooquity.jar -port 2202 -webadmin > nohup.out 2>&1&

Please add this tip to the FAQ page.
Tom, if you work on externalizing the JavaScript so that skinners can add custom client side actions in the future I will rewrite the default scripts to see if I can get better performance across all browsers. What do you think?
Tom, thank you for telling us about Ubooquity using the working directory. I will try to run the jar from my storage volume in a few minutes and report back.
I do not have a Seagate NAS, but I can give some general advice. First you must enable access to the device through a protocol called SSH. Follow this quick tutorial to enable SSH. Next download Putty open it then give it the IP address of your NAS. Log in with an admin account or 'root' if you have the root password.

Seagate says that it doesn't use alot of Linux commands so I'm not sure what will work for you. The next general steps will be to install Java 7 or above, downloading Ubooquity, unzipping Ubooquity then running Ubooquity. You might be able to install Java through the Seagate web interface.

Make a directory to hold Ubooquity then move in to it
mkdir /var/packages/Ubooquity
cd /var/packages/Ubooquity
Download Ubooquity
wget http://vaemendis.net/ubooquity/service/download.php
Unzip the package you downloaded
unzip download.php
Start the server
java -jar Ubooquity.jar -webadmin
If the server started you should be able to view the web interface by putting the IP address of your NAS in to a browser and adding :2202 to the end.
When the program scrapes all of your comics it is saving the selected metadata from its tags in to the Ubooquity database. Tom wrote above that making the scraper also look for publisher information would require that every user do a full rescan of their collection because the database does not currently save that metadata tag. Adding support for plot, release year and other tags will do the same: require a full rescan if Tom implements them.

I'm with you, Hayden. I'd like Ubooquity to be more like Kodi and show issue details. I hope that inclusion of more metadata goes hand-in-hand with progress on the user interface to make it as intuitive and pleasant as other front-ends (Kodi, Plex).

For showing the number of issues that is as simple as counting the number of files in the current folder, but I think you mean to show the number of published issues for the series you are viewing, right? For continuing series this changes every month and would require Ubooquity to have an internet connection, a ComicVine API key and to scrape the API continuously. Sounds bad. This is directly related to your request of having a reporting feature because users would have to be able to see placeholder empty issues where an issue is expected, but does not exist which would require Ubooquity to scrape ComicVine for a full list of every published issue then correctly insert into place, or otherwise be able to show the user where they are missing issues. ComicRack is supposed to have a plugin that shows you series gaps, but I've never been able to get it to work. I have a feeling Tom will say this missing issue business is outside the scope of his program. Let's wait and see :)
Comic Tagger is good, but if I remember correctly, doesn't let you preview the cover before deciding on the volume. I suggest you install ComicRack with the ComicVine scraper plugin. The options in ComicRack are really good. You can even set character replacement for illegal characters when the program exports or renames your comics.