It sounds like your cycle is going pretty smoothely, the only things i would like to add on the subject of cycling tanks is that its advised that you do a small water change any time you see ammonia or nitrites, this will slow the cycling of the tank down in the long term if you do this, but on the other hand its not adviseable to let nitrites or ammonia to build up as they are toxic to fish. Ultimately, the welfare of the fish is what is most important when doing a cycle with fish, so i would advise doing a small water change anytime you see ammonia or nitrites

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Cycling with fish does take longer than doing a fishless cycle (i.e. cycling the tank with pure ammonia instead of relying on fish to provide the ammonia source) and tanks which are cycling with fish tend to take longer to establish. Generally speaking, most tanks cycled with fish take 3months on average until the cycle is complete, and 6months until the tank is fully established/mature (when a tank is fully established/mature, the chances of water quality problems/unstable water quality occuring is extremely slim).
The live bacteria the guy at the petshop gave you is a controverisal stuff- a lot of the time it does not work at all. The beneficical bacteria found in the tank filter to survive need;
a. Oxygen
b. Ammonia
c. Flowing water to deliver them the oxygen and ammonia they need to survive
d. Surfaces for the bacteria to live on
The problem with the bottled bacteria stuff, is that in bottle conditions it has none of these things. Refrigerating the bacteria can put it into a dormant state and keep it alive for a long time without these factors, but on the other hand, most bottled live bacteria tends not to be refrigerated at petshops, so ultimately i don't know how it can survive- some people claim seeing their cycle speeded up when they add the bottled bacteria, but scientifically i don't see how this could happen unless it was purely a matter of the dead bacteria mixture decomposing in the filter and producing some ammonia for newly establishing bacteria in the tank to live off.
So the bottled bacteria thing is a bit of a controversial issue, a lot of people can't see how the stuff could actually work. The filter bacteria though needs a constant source of ammonia to survive though, so by adding it to the tank a couple of days before you added fish, any bacteria still alive in the bottle would have died off by the time you added the fish.
With the amano shrimp though (they are also known by other names like Bamboo and Japonica shrimp, the name "Amano" comes from the famous tank designer Takeshi Amano who had the shrimp named after him), i wouldn't add the shrimp until after the tank has finished cycling as they really are too sensitive to nitrites and ammonia to risk being put into a cycling tank.
I think there are other types of shrimp like ghost shrimp, which i think are more hardy than amano shrimp, but as far as i know shrimp in general are pretty sensitive to water quality conditions, so its best only to add them once the tanks water quality has settled down and become good and stable

. The shrimp will add to the bioload of the tank, but their effect on the bioload of the tank will be pretty small.
In the mean time though with the uneaten food on the substrate problem, until you get the shrimps, moving a net close and just above to the surface of the sand substrate is a good way to clean any uneaten food off the substrate as the food will rise off the substrate if you create some water movement near it with a net so it can easily be netted up

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With the betta following the molly around, is he flaring at the molly at all? "Flaring" is when a male betta puffs out special gill flaps like this;
http
/farm1.static.flickr.com/74/169373972_a532eb3909.jpg
http
/www.cbsbettas.org/images/betta.jpg
http
/www.akvariumas.lt/zuvys/belontiidae...lendens_big.jpg
Its can be both either an agressive and a defensive behavior or both- in the wild male bettas are very intolerant of each other, they will try to stake out a territory of their own and defend it. If other male bettas (or unwanted female bettas) stray into the male bettas territory, he will flare at them to warn them off- if they do not retreat, he will then attack the intruder.
If your betta is flaring at the mollys, he is probably stressed out by their presence and it would probably be best to separate the betta from the mollys.
Getting a 2gal tank for bettas needn't be expensive- you can buy cheap 10 litre containers like this which could be used to house a betta, only costing £2.60;
http
/cgi.ebay.co.uk/10-litre-plastic-foo...1QQcmdZViewItem
10 litres would be 2.64gallons, its not the prettiest thing you could put a betta in, but its more than large enough to house a single betta. Filtration is not nesarsary if you do once daily 100% water changes, and heating is not nesarsary as long as the temp of the tub/tank stays around a more or less constant room temp of around 24degrees or more. Bettas are one of the few tropical fish that can be kept in such conditions, their habitat in the wild tends to be ponds or rivers with minimal or no water flow, they're pretty tough fish in some ways and can live in a variety of water conditions as long as their habitat is suited to them and tank mates are chosen with a lot of care (although often ideally, no tank mates at all is the best due to male bettas generally unsociable nature)

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With the molly on the substrate not doing much, is it showing any other symptomes whether behvioral or physical i.e. fish is bloated looking, skinny looking/has sunken stomach, is gasping, has unusual growths on it like spots, cotton wool like growths, slimey substance covering it etc, tattered/ragged looking fins, fish is flicking/rubbing itself on objects etc etc?
The first thing i would do though is test the water for ammonia, nitrites and nitrates and post the results here

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