Good evening,
It's been a while since I covered this subject at school so I'm a little rusty. I seem to recall though that they had been there for some time before meeting the first indigenous people. As the series only covers a 2 week period of time then we are not going to see them.
....... and still no guard.
Major Scott? would be better off improving his military skills rather than his bedside skills.

Re NO Guard ..... there was actually no garrison force sent out .... the marines were charged with the responsibility to guard during the voyage, but in a formal sense they had no authority once they had supervised the landing of the convicts.... And many of the RN knew this technical legality .... it caused the NSW Governor some significant hassles....

Re Major SCOTT .... who was he?
My school girl memories have
Major Robert Ross,
his Adjutant, Second Lieutenant John Long,
Quartermaster Lieutenant James Furzer,
Engineer Officer Lieutenant William Dawes and his four Company Commanders,
Captains James Campbell and John Shea and
Captain Lieutenants James Meredith and Watkin Tench.
Has Sergeant James SCOTT become a Major ......
http://en.wikipedia.org/wiki/Journals_of_the_First_Fleet#James_Scott

First meetings of the two cultures: From Day 1

and available online for Jimmy McGovern to draw upon....
"18 January: After a voyage of eight months from Portsmouth in England, 11 sailing ships, carrying officers, sailors, male and female convicts and marines and their wives assemble at Botany Bay. To avoid a large group of Gweagal at Kundul, Captain Arthur Phillip, the first governor of a planned convict colony, lands at Kamay on the north shore. Aboriginal people show Phillip where to find water.
22 January: Phillip takes two cutters and a longboat to explore Port Jackson. Impressed by young warriors at Kayeemy, he renames it Manly Cove. While the English are eating, Phillip draws a circle around them in the sand. This ‘line in the sand’, secured by marines armed with muskets, sets up a physical and symbolic barrier between the Indigenous people and the English at their first meeting.
23 January: The English party spends two nights in tents on the beach at Cadi (Camp Cove, near Watsons Bay), heartland of the harbour-dwelling Cadigal (Grass Tree Clan). Phillip decides to abandon Botany Bay and establish the settlement at the spacious harbour of Port Jackson.
At Botany Bay, the red-coated British marines, who carry long-barrelled Brown Bess muskets, awe the Gweagal and Kameygal.
‘I am well convinced that they know and dread the superiority of our arms,‘ writes Surgeon John White, adding, ‘from the first, they carefully avoided a soldier, or any person wearing a red coat, which they seem to have marked as a fighting venture’. White sees Botany Bay warriors painted with stripes across the chest and back ‘which at some little distance appears not unlike our soldiers’ cross belts’."Source: John White, Journal of a Voyage to New South Wales, London: Debrett, 1790:118. John White’s Journal is available online as a Project Gutenberg of Australia e-Book.
http://k6.boardofstudies.nsw.edu.au/wps/portal/go/hsie/background-sheets/british-colonisers-1770-1792#1788