I think the main advantage of using sentences is that it gives you vocabulary and grammar points right there, in real Japanese, without having to drill those things separately.
If you are having trouble remembering particular things, it can help to just study those things the old fashioned way, outside of the SRS, in order to help get it into your memory. If there are particular words or grammar points that keep getting you confused, you can also add more cards that use it.

Only tip I have to offer is to add more sentences that contain words you have trouble with.  Or read stuff, whatever, I don't care.  The important thing is to see things in a lot of different contexts, since that's important for making things "click".  I can speak from experience on that; I had trouble with words like 飛行機 and 郵便局 when they only showed up once in my deck.

I'm sure I've been through both at some point.

You just need more sentences and more time.  When your deck gets larger there is a lot more cross referencing going on, so just keep adding sentences.  Separate vocabulary word cards usually are more difficult to remember than those words in sentences.  A grammar card is the same as a sentence card.  All sentences contain grammar, so perhaps just add a lot of sentences with the grammar you are studying at that time.  It will be obvious what grammar point the sentence is displaying.

As for writing, it's up to you.  I think as a beginner you don't even need to write them down at all yet.  Just keep up your Heisig reviews until they get to a low number per day.  What you need is a large amount of vocab and basic grammar crammed into your brain in a short time.  So just doing recognition will speed this up until you have the basics.  Your immersion will also be less effective unless you quickly get some words and phrases into your passive vocabulary.

There are methods for remembering the on yomi.
For instance, the http://drmoviemethod.blogspot.com/ was already discussed in many posts here in the forum.