My nitro and nifedipine comes in a jar/tub too but I used a baby syringe like this one to suck some up so I can get it further up the anal canal:
http://s3.amazonaws.com/tc-photos/11442/product/standard/513141.jpg
What I did is turn the jar upside down and shake it a few times until some of the ointment falls onto the inside of the lid. Then I open the lid and suck it up using the syringe.
I think the possible impacts of long term stool softener use will depend on what kind (e.g., stimulant, osmotic, etc.) you are using. In general all medical literature agrees that stimulant laxatives should not be used long term. Osmotics like Miralax are considered safe, or at least safer. One reason that the Miralax bottle says not to use it for more than 14 days is because they don't want people to use it to mask the symptoms of very serious conditions that can cause constipation, such as intestinal blockage or colon cancer. If you've been cleared of these conditions and it's just "standard" (whatever that is) constipation, then it's generally considered okay from everyone and everything I've consulted. That doesn't mean there's no impact at all but it does mean it's unlikely to cause major life-threatening trouble.

That syringe is ideal because of the tapered end, I have a syringe that is used for giving medicine to babies and children, it's not tapered but is quite slim and should be easy to pop up the anus with the aid of a little vaseline so I might just try that.
The stool softeners i'm taking are docusate sodium but I also have some macrogol sachets (movicol) as back up, i've been taking these kind of stool softeners for over a year now, at first I started off with lactulose 4-5 times a day which didn't really help so the GP then prescribed me movicol and docusate sodium so I use any or both as required

Yup I know the baby medicine syringes you speak of, I have two 5-month old twins at home and one of them has a serious medical condition that requires giving him drugs orally every day. Those syringes should actually work just as well, and since they should be divided into 10ths of a millimeter, they should allow you to be a bit more accurate with dosage. With my big syringe, there were times when I shot in waaaaay too much nitro and nearly fainted lol.

Ha ha ha Neuro LOL - If I knew I could "knock-out" myself with Nitro - I definitely would have been tempted to do so in the worst periods of my "fissure-life" LMAO